Error during MAVIS setup #246

sarahdada · 2021-04-27T18:01:24Z

Describe the bug
This bug shows the following error during setup, it might be an issue with parsing. I am running manta-1.4.0 , the data might be in the wrong format.

To Reproduce
Steps to reproduce the behavior: .cfg file was made using the commands
mavis config
--library PG00038 genome normal False hg38_PG1.bam
--library PG00037 genome normal False hg38_PG2.bam
--library PG00048 genome diseased False hg38_PG3.bam
--convert delly PG_dellysomatic_hg38.vcf delly
--convert manta diploidSV.de_novo.vcf manta
--assign PG1 delly manta
--assign PG2 delly manta
--assign PG3 delly manta
-w PG0001_2_3.cfg

The problem

run command 'mavis setup PG0001_2_3.cfg -o path/to/results'
See error ...
File "/home/user/miniconda3/bin/mavis", line 8, in
sys.exit(main())
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/main.py", line 600, in main
raise err
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/main.py", line 582, in main
pipeline = _pipeline.Pipeline.build(config)
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/schedule/pipeline.py", line 350, in build
libconf.inputs = run_conversion(config, libconf, conversion_dir)
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/schedule/pipeline.py", line 81, in run_conversion
convert_tool_output(
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/tools/init.py", line 34, in convert_tool_output
_convert_tool_output(
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/tools/init.py", line 276, in _convert_tool_output
rows = read_vcf(input_file, file_type, log)
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 197, in convert_file
raise err
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 194, in convert_file
rows.extend(convert_record(vcf_record, log=log))
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 110, in convert_record
chr2, end, orient1, orient2, ref, alt = parse_bnd_alt(alt)
File "/home/user/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 74, in parse_bnd_alt
raise NotImplementedError('alt specification in unexpected format', alt)
NotImplementedError: ('alt specification in unexpected format', ']chr19:27302623]')

Expected behavior
Consolidation of SV data

Versions (please complete the following information):

OS: centos-07
Python Version 3.8.3
MAVIS 2.2.9
Blat

Additional context
Add any other context about the problem here.

creisle · 2021-04-28T21:21:06Z

@sarahdada could you include the vcf header and variant line in question? Which file did the error occur on (should have a log message for which one it was converting above the error)

To get the relevant lines you can use grep

grep 'chr19:27302623' diploidSV.de_novo.vcf

and the header

grep '^##' diploidSV.de_novo.vcf

Make sure to remove any identifiers before posting (library names, patient names, etc)

sarahdada · 2021-04-28T21:30:14Z

For grep chr19, it doesn't seem to come up with anything- so maybe the SV caller format is off

##fileformat=VCFv4.1
##fileDate=20210415
##source=GenerateSVCandidates 1.4.0
##reference=file:///projects/file/hg38_no_alt.fa
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chrM,length=16569>
##contig=<ID=chr1_KI270706v1_random,length=175055>
##contig=<ID=chr1_KI270707v1_random,length=32032>
##contig=<ID=chr1_KI270708v1_random,length=127682>
##contig=<ID=chr1_KI270709v1_random,length=66860>
##contig=<ID=chr1_KI270710v1_random,length=40176>
##contig=<ID=chr1_KI270711v1_random,length=42210>
##contig=<ID=chr1_KI270712v1_random,length=176043>
##contig=<ID=chr1_KI270713v1_random,length=40745>
##contig=<ID=chr1_KI270714v1_random,length=41717>
##contig=<ID=chr2_KI270715v1_random,length=161471>
##contig=<ID=chr2_KI270716v1_random,length=153799>
##contig=<ID=chr3_GL000221v1_random,length=155397>
##contig=<ID=chr4_GL000008v2_random,length=209709>
##contig=<ID=chr5_GL000208v1_random,length=92689>
##contig=<ID=chr9_KI270717v1_random,length=40062>
##contig=<ID=chr9_KI270718v1_random,length=38054>
##contig=<ID=chr9_KI270719v1_random,length=176845>
##contig=<ID=chr9_KI270720v1_random,length=39050>
##contig=<ID=chr11_KI270721v1_random,length=100316>
##contig=<ID=chr14_GL000009v2_random,length=201709>
##contig=<ID=chr14_GL000225v1_random,length=211173>
##contig=<ID=chr14_KI270722v1_random,length=194050>
##contig=<ID=chr14_GL000194v1_random,length=191469>
##contig=<ID=chr14_KI270723v1_random,length=38115>
##contig=<ID=chr14_KI270724v1_random,length=39555>
##contig=<ID=chr14_KI270725v1_random,length=172810>
##contig=<ID=chr14_KI270726v1_random,length=43739>
##contig=<ID=chr15_KI270727v1_random,length=448248>
##contig=<ID=chr16_KI270728v1_random,length=1872759>
##contig=<ID=chr17_GL000205v2_random,length=185591>
##contig=<ID=chr17_KI270729v1_random,length=280839>
##contig=<ID=chr17_KI270730v1_random,length=112551>
##contig=<ID=chr22_KI270731v1_random,length=150754>
##contig=<ID=chr22_KI270732v1_random,length=41543>
##contig=<ID=chr22_KI270733v1_random,length=179772>
##contig=<ID=chr22_KI270734v1_random,length=165050>
##contig=<ID=chr22_KI270735v1_random,length=42811>
##contig=<ID=chr22_KI270736v1_random,length=181920>
##contig=<ID=chr22_KI270737v1_random,length=103838>
##contig=<ID=chr22_KI270738v1_random,length=99375>
##contig=<ID=chr22_KI270739v1_random,length=73985>
##contig=<ID=chrY_KI270740v1_random,length=37240>
##contig=<ID=chrUn_KI270302v1,length=2274>
##contig=<ID=chrUn_KI270304v1,length=2165>
##contig=<ID=chrUn_KI270303v1,length=1942>
##contig=<ID=chrUn_KI270305v1,length=1472>
##contig=<ID=chrUn_KI270322v1,length=21476>
##contig=<ID=chrUn_KI270320v1,length=4416>
##contig=<ID=chrUn_KI270310v1,length=1201>
##contig=<ID=chrUn_KI270316v1,length=1444>
##contig=<ID=chrUn_KI270315v1,length=2276>
##contig=<ID=chrUn_KI270312v1,length=998>
##contig=<ID=chrUn_KI270311v1,length=12399>
##contig=<ID=chrUn_KI270317v1,length=37690>
##contig=<ID=chrUn_KI270412v1,length=1179>
##contig=<ID=chrUn_KI270411v1,length=2646>
##contig=<ID=chrUn_KI270414v1,length=2489>
##contig=<ID=chrUn_KI270419v1,length=1029>
##contig=<ID=chrUn_KI270418v1,length=2145>
##contig=<ID=chrUn_KI270420v1,length=2321>
##contig=<ID=chrUn_KI270424v1,length=2140>
##contig=<ID=chrUn_KI270417v1,length=2043>
##contig=<ID=chrUn_KI270422v1,length=1445>
##contig=<ID=chrUn_KI270423v1,length=981>
##contig=<ID=chrUn_KI270425v1,length=1884>
##contig=<ID=chrUn_KI270429v1,length=1361>
##contig=<ID=chrUn_KI270442v1,length=392061>
##contig=<ID=chrUn_KI270466v1,length=1233>
##contig=<ID=chrUn_KI270465v1,length=1774>
##contig=<ID=chrUn_KI270467v1,length=3920>
##contig=<ID=chrUn_KI270435v1,length=92983>
##contig=<ID=chrUn_KI270438v1,length=112505>
##contig=<ID=chrUn_KI270468v1,length=4055>
##contig=<ID=chrUn_KI270510v1,length=2415>
##contig=<ID=chrUn_KI270509v1,length=2318>
##contig=<ID=chrUn_KI270518v1,length=2186>
##contig=<ID=chrUn_KI270508v1,length=1951>
##contig=<ID=chrUn_KI270516v1,length=1300>
##contig=<ID=chrUn_KI270512v1,length=22689>
##contig=<ID=chrUn_KI270519v1,length=138126>
##contig=<ID=chrUn_KI270522v1,length=5674>
##contig=<ID=chrUn_KI270511v1,length=8127>
##contig=<ID=chrUn_KI270515v1,length=6361>
##contig=<ID=chrUn_KI270507v1,length=5353>
##contig=<ID=chrUn_KI270517v1,length=3253>
##contig=<ID=chrUn_KI270529v1,length=1899>
##contig=<ID=chrUn_KI270528v1,length=2983>
##contig=<ID=chrUn_KI270530v1,length=2168>
##contig=<ID=chrUn_KI270539v1,length=993>
##contig=<ID=chrUn_KI270538v1,length=91309>
##contig=<ID=chrUn_KI270544v1,length=1202>
##contig=<ID=chrUn_KI270548v1,length=1599>
##contig=<ID=chrUn_KI270583v1,length=1400>
##contig=<ID=chrUn_KI270587v1,length=2969>
##contig=<ID=chrUn_KI270580v1,length=1553>
##contig=<ID=chrUn_KI270581v1,length=7046>
##contig=<ID=chrUn_KI270579v1,length=31033>
##contig=<ID=chrUn_KI270589v1,length=44474>
##contig=<ID=chrUn_KI270590v1,length=4685>
##contig=<ID=chrUn_KI270584v1,length=4513>
##contig=<ID=chrUn_KI270582v1,length=6504>
##contig=<ID=chrUn_KI270588v1,length=6158>
##contig=<ID=chrUn_KI270593v1,length=3041>
##contig=<ID=chrUn_KI270591v1,length=5796>
##contig=<ID=chrUn_KI270330v1,length=1652>
##contig=<ID=chrUn_KI270329v1,length=1040>
##contig=<ID=chrUn_KI270334v1,length=1368>
##contig=<ID=chrUn_KI270333v1,length=2699>
##contig=<ID=chrUn_KI270335v1,length=1048>
##contig=<ID=chrUn_KI270338v1,length=1428>
##contig=<ID=chrUn_KI270340v1,length=1428>
##contig=<ID=chrUn_KI270336v1,length=1026>
##contig=<ID=chrUn_KI270337v1,length=1121>
##contig=<ID=chrUn_KI270363v1,length=1803>
##contig=<ID=chrUn_KI270364v1,length=2855>
##contig=<ID=chrUn_KI270362v1,length=3530>
##contig=<ID=chrUn_KI270366v1,length=8320>
##contig=<ID=chrUn_KI270378v1,length=1048>
##contig=<ID=chrUn_KI270379v1,length=1045>
##contig=<ID=chrUn_KI270389v1,length=1298>
##contig=<ID=chrUn_KI270390v1,length=2387>
##contig=<ID=chrUn_KI270387v1,length=1537>
##contig=<ID=chrUn_KI270395v1,length=1143>
##contig=<ID=chrUn_KI270396v1,length=1880>
##contig=<ID=chrUn_KI270388v1,length=1216>
##contig=<ID=chrUn_KI270394v1,length=970>
##contig=<ID=chrUn_KI270386v1,length=1788>
##contig=<ID=chrUn_KI270391v1,length=1484>
##contig=<ID=chrUn_KI270383v1,length=1750>
##contig=<ID=chrUn_KI270393v1,length=1308>
##contig=<ID=chrUn_KI270384v1,length=1658>
##contig=<ID=chrUn_KI270392v1,length=971>
##contig=<ID=chrUn_KI270381v1,length=1930>
##contig=<ID=chrUn_KI270385v1,length=990>
##contig=<ID=chrUn_KI270382v1,length=4215>
##contig=<ID=chrUn_KI270376v1,length=1136>
##contig=<ID=chrUn_KI270374v1,length=2656>
##contig=<ID=chrUn_KI270372v1,length=1650>
##contig=<ID=chrUn_KI270373v1,length=1451>
##contig=<ID=chrUn_KI270375v1,length=2378>
##contig=<ID=chrUn_KI270371v1,length=2805>
##contig=<ID=chrUn_KI270448v1,length=7992>
##contig=<ID=chrUn_KI270521v1,length=7642>
##contig=<ID=chrUn_GL000195v1,length=182896>
##contig=<ID=chrUn_GL000219v1,length=179198>
##contig=<ID=chrUn_GL000220v1,length=161802>
##contig=<ID=chrUn_GL000224v1,length=179693>
##contig=<ID=chrUn_KI270741v1,length=157432>
##contig=<ID=chrUn_GL000226v1,length=15008>
##contig=<ID=chrUn_GL000213v1,length=164239>
##contig=<ID=chrUn_KI270743v1,length=210658>
##contig=<ID=chrUn_KI270744v1,length=168472>
##contig=<ID=chrUn_KI270745v1,length=41891>
##contig=<ID=chrUn_KI270746v1,length=66486>
##contig=<ID=chrUn_KI270747v1,length=198735>
##contig=<ID=chrUn_KI270748v1,length=93321>
##contig=<ID=chrUn_KI270749v1,length=158759>
##contig=<ID=chrUn_KI270750v1,length=148850>
##contig=<ID=chrUn_KI270751v1,length=150742>
##contig=<ID=chrUn_KI270752v1,length=27745>
##contig=<ID=chrUn_KI270753v1,length=62944>
##contig=<ID=chrUn_KI270754v1,length=40191>
##contig=<ID=chrUn_KI270755v1,length=36723>
##contig=<ID=chrUn_KI270756v1,length=79590>
##contig=<ID=chrUn_KI270757v1,length=71251>
##contig=<ID=chrUn_GL000214v1,length=137718>
##contig=<ID=chrUn_KI270742v1,length=186739>
##contig=<ID=chrUn_GL000216v2,length=176608>
##contig=<ID=chrUn_GL000218v1,length=161147>
##contig=<ID=chrEBV,length=171823>
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
##INFO=<ID=JUNCTION_QUAL,Number=1,Type=Integer,Description="If the SV junction is part of an EVENT (ie. a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only">
##FORMAT=<ID=DQ,Number=1,Type=Integer,Description="De novo quality score">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999">
##FILTER=<ID=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation">
##FILTER=<ID=MaxDepth,Description="Depth is greater than 3x the median chromosome depth near one or both variant breakends">
##FILTER=<ID=MaxMQ0Frac,Description="For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4">
##FILTER=<ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample.">
##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20">
##FILTER=<ID=MinGQ,Description="GQ score is less than 15 (filter applied at sample level and record level if all samples are filtered)">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##cmdline=/gsc/software/linux-x86_64-centos6/manta-1.4.0/bin/configManta.py --bam /projects/bam /projects/path//file1.bam --bam /projects/path/file2.bam --bam /projects/bam /projects/path/file3.bam --referenceFasta /projects/path/hg38_no_alt.fa --runDir /projects/path/MantaResults_withHeader/ ```

sarahdada · 2021-04-28T21:37:12Z

The error comes when:

(base) [sdada@gphost14 MAVIS]$ mavis setup file.cfg -o /path/MAVIS
MAVIS: 2.2.9
hostname: gphost14.bcgsc.ca
[2021-04-28 14:39:13] arguments
command = 'setup'
config = '/projects/path/file.cfg'
log = None
log_level = 'INFO'
output = '/projects/path/MAVIS'
skip_stage = []
creating output directory: '/projects/path/MAVIS/converted_inputs'
setting up the directory structure for PG0003838 as /projects/path/MAVIS/PG0003_normal_genome
converting input command: ['convert_tool_output', '/projects/filepath/file1.vcf', 'delly', False]
reading: /projects/file1.vcf

Header for DELLY

(base) [sdada@gphost14 hg38_PG0003514_3838_4859_fastq_SV]$ grep '^#' file.vcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20210412
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Translocation">
##ALT=<ID=INS,Description="Insertion">
##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">
##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
##FORMAT=<ID=RDCN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
##reference=/projects/sdada_prj/sdada_scratch/MSSNG/yingsfiles/hg38_no_alt.fa
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
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##contig=<ID=chr1_KI270709v1_random,length=66860>
##contig=<ID=chr1_KI270710v1_random,length=40176>
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##contig=<ID=chr1_KI270713v1_random,length=40745>
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##contig=<ID=chr9_KI270719v1_random,length=176845>
##contig=<ID=chr9_KI270720v1_random,length=39050>
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##contig=<ID=chr22_KI270735v1_random,length=42811>
##contig=<ID=chr22_KI270736v1_random,length=181920>
##contig=<ID=chr22_KI270737v1_random,length=103838>
##contig=<ID=chr22_KI270738v1_random,length=99375>
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##contig=<ID=chrY_KI270740v1_random,length=37240>
##contig=<ID=chrUn_KI270302v1,length=2274>
##contig=<ID=chrUn_KI270304v1,length=2165>
##contig=<ID=chrUn_KI270303v1,length=1942>
##contig=<ID=chrUn_KI270305v1,length=1472>
##contig=<ID=chrUn_KI270322v1,length=21476>
##contig=<ID=chrUn_KI270320v1,length=4416>
##contig=<ID=chrUn_KI270310v1,length=1201>
##contig=<ID=chrUn_KI270316v1,length=1444>
##contig=<ID=chrUn_KI270315v1,length=2276>
##contig=<ID=chrUn_KI270312v1,length=998>
##contig=<ID=chrUn_KI270311v1,length=12399>
##contig=<ID=chrUn_KI270317v1,length=37690>
##contig=<ID=chrUn_KI270412v1,length=1179>
##contig=<ID=chrUn_KI270411v1,length=2646>
##contig=<ID=chrUn_KI270414v1,length=2489>
##contig=<ID=chrUn_KI270419v1,length=1029>
##contig=<ID=chrUn_KI270418v1,length=2145>
##contig=<ID=chrUn_KI270420v1,length=2321>
##contig=<ID=chrUn_KI270424v1,length=2140>
##contig=<ID=chrUn_KI270417v1,length=2043>
##contig=<ID=chrUn_KI270422v1,length=1445>
##contig=<ID=chrUn_KI270423v1,length=981>
##contig=<ID=chrUn_KI270425v1,length=1884>
##contig=<ID=chrUn_KI270429v1,length=1361>
##contig=<ID=chrUn_KI270442v1,length=392061>
##contig=<ID=chrUn_KI270466v1,length=1233>
##contig=<ID=chrUn_KI270465v1,length=1774>
##contig=<ID=chrUn_KI270467v1,length=3920>
##contig=<ID=chrUn_KI270435v1,length=92983>
##contig=<ID=chrUn_KI270438v1,length=112505>
##contig=<ID=chrUn_KI270468v1,length=4055>
##contig=<ID=chrUn_KI270510v1,length=2415>
##contig=<ID=chrUn_KI270509v1,length=2318>
##contig=<ID=chrUn_KI270518v1,length=2186>
##contig=<ID=chrUn_KI270508v1,length=1951>
##contig=<ID=chrUn_KI270516v1,length=1300>
##contig=<ID=chrUn_KI270512v1,length=22689>
##contig=<ID=chrUn_KI270519v1,length=138126>
##contig=<ID=chrUn_KI270522v1,length=5674>
##contig=<ID=chrUn_KI270511v1,length=8127>
##contig=<ID=chrUn_KI270515v1,length=6361>
##contig=<ID=chrUn_KI270507v1,length=5353>
##contig=<ID=chrUn_KI270517v1,length=3253>
##contig=<ID=chrUn_KI270529v1,length=1899>
##contig=<ID=chrUn_KI270528v1,length=2983>
##contig=<ID=chrUn_KI270530v1,length=2168>
##contig=<ID=chrUn_KI270539v1,length=993>
##contig=<ID=chrUn_KI270538v1,length=91309>
##contig=<ID=chrUn_KI270544v1,length=1202>
##contig=<ID=chrUn_KI270548v1,length=1599>
##contig=<ID=chrUn_KI270583v1,length=1400>
##contig=<ID=chrUn_KI270587v1,length=2969>
##contig=<ID=chrUn_KI270580v1,length=1553>
##contig=<ID=chrUn_KI270581v1,length=7046>
##contig=<ID=chrUn_KI270579v1,length=31033>
##contig=<ID=chrUn_KI270589v1,length=44474>
##contig=<ID=chrUn_KI270590v1,length=4685>
##contig=<ID=chrUn_KI270584v1,length=4513>
##contig=<ID=chrUn_KI270582v1,length=6504>
##contig=<ID=chrUn_KI270588v1,length=6158>
##contig=<ID=chrUn_KI270593v1,length=3041>
##contig=<ID=chrUn_KI270591v1,length=5796>
##contig=<ID=chrUn_KI270330v1,length=1652>
##contig=<ID=chrUn_KI270329v1,length=1040>
##contig=<ID=chrUn_KI270334v1,length=1368>
##contig=<ID=chrUn_KI270333v1,length=2699>
##contig=<ID=chrUn_KI270335v1,length=1048>
##contig=<ID=chrUn_KI270338v1,length=1428>
##contig=<ID=chrUn_KI270340v1,length=1428>
##contig=<ID=chrUn_KI270336v1,length=1026>
##contig=<ID=chrUn_KI270337v1,length=1121>
##contig=<ID=chrUn_KI270363v1,length=1803>
##contig=<ID=chrUn_KI270364v1,length=2855>
##contig=<ID=chrUn_KI270362v1,length=3530>
##contig=<ID=chrUn_KI270366v1,length=8320>
##contig=<ID=chrUn_KI270378v1,length=1048>
##contig=<ID=chrUn_KI270379v1,length=1045>
##contig=<ID=chrUn_KI270389v1,length=1298>
##contig=<ID=chrUn_KI270390v1,length=2387>
##contig=<ID=chrUn_KI270387v1,length=1537>
##contig=<ID=chrUn_KI270395v1,length=1143>
##contig=<ID=chrUn_KI270396v1,length=1880>
##contig=<ID=chrUn_KI270388v1,length=1216>
##contig=<ID=chrUn_KI270394v1,length=970>
##contig=<ID=chrUn_KI270386v1,length=1788>
##contig=<ID=chrUn_KI270391v1,length=1484>
##contig=<ID=chrUn_KI270383v1,length=1750>
##contig=<ID=chrUn_KI270393v1,length=1308>
##contig=<ID=chrUn_KI270384v1,length=1658>
##contig=<ID=chrUn_KI270392v1,length=971>
##contig=<ID=chrUn_KI270381v1,length=1930>
##contig=<ID=chrUn_KI270385v1,length=990>
##contig=<ID=chrUn_KI270382v1,length=4215>
##contig=<ID=chrUn_KI270376v1,length=1136>
##contig=<ID=chrUn_KI270374v1,length=2656>
##contig=<ID=chrUn_KI270372v1,length=1650>
##contig=<ID=chrUn_KI270373v1,length=1451>
##contig=<ID=chrUn_KI270375v1,length=2378>
##contig=<ID=chrUn_KI270371v1,length=2805>
##contig=<ID=chrUn_KI270448v1,length=7992>
##contig=<ID=chrUn_KI270521v1,length=7642>
##contig=<ID=chrUn_GL000195v1,length=182896>
##contig=<ID=chrUn_GL000219v1,length=179198>
##contig=<ID=chrUn_GL000220v1,length=161802>
##contig=<ID=chrUn_GL000224v1,length=179693>
##contig=<ID=chrUn_KI270741v1,length=157432>
##contig=<ID=chrUn_GL000226v1,length=15008>
##contig=<ID=chrUn_GL000213v1,length=164239>
##contig=<ID=chrUn_KI270743v1,length=210658>
##contig=<ID=chrUn_KI270744v1,length=168472>
##contig=<ID=chrUn_KI270745v1,length=41891>
##contig=<ID=chrUn_KI270746v1,length=66486>
##contig=<ID=chrUn_KI270747v1,length=198735>
##contig=<ID=chrUn_KI270748v1,length=93321>
##contig=<ID=chrUn_KI270749v1,length=158759>
##contig=<ID=chrUn_KI270750v1,length=148850>
##contig=<ID=chrUn_KI270751v1,length=150742>
##contig=<ID=chrUn_KI270752v1,length=27745>
##contig=<ID=chrUn_KI270753v1,length=62944>
##contig=<ID=chrUn_KI270754v1,length=40191>
##contig=<ID=chrUn_KI270755v1,length=36723>
##contig=<ID=chrUn_KI270756v1,length=79590>
##contig=<ID=chrUn_KI270757v1,length=71251>
##contig=<ID=chrUn_GL000214v1,length=137718>
##contig=<ID=chrUn_KI270742v1,length=186739>
##contig=<ID=chrUn_GL000216v2,length=176608>
##contig=<ID=chrUn_GL000218v1,length=161147>
##contig=<ID=chrEBV,length=171823>
##bcftools_viewVersion=1.11+htslib-1.11
##bcftools_viewCommand=view -Ov PG0004859-BLD_PG0003514compared_dellysomatic_hg38.bcf; Date=Thu Apr 22 11:38:25 2021
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PG0004859-BLD_hg38_marked_dup PG0003514-BLD_hg38_marked_dup

DELLY vcf grep chr19 does get a result. I can't scroll up on error but can just quickly rerun

chrUn_KI270516v1        2       BND00073768     N       ]chr19:27302623]        67      LowQual PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.7;END=3;CHR2=chr19;POS2=27302623;PE=0;MAPQ=0;CT=5to3;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=14;INSLEN=0;HOMLEN=0;SR=4;SRQ=0.951613;CONSENSUS=CAATTTGGAGAGTTTTGAGGCCTATTGTGGAAAGATATATCCTAAAATAAAAAATACACGGAAGCATTCTGAGAAACTTCATTGTTTTGTGTGCATTCAACTCACAGAGTTGAACCTATCT;CE=1.9285GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV  0/1:-129.223,0,-44.7728:10000:PASS:0:110747:110747:2:0:0:19:59  0/1:-107.543,0,-42.0154:10000:PASS:0:95614:95614:2:0:0:16:41


(base) [sdada@gphost14 DellyResults_withHeader]$ grep 'chr19:27302623' dellyfile2.vcf
chrUn_KI270516v1        2       BND00069701     N       ]chr19:27302623]        67      LowQual PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.7;END=3;CHR2=chr19;POS2=27302623;PE=0;MAPQ=0;CT=5to3;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=14;INSLEN=0;HOMLEN=0;SR=4;SRQ=0.951613;CONSENSUS=CAATTTGGAGAGTTTTGAGGCCTATTGTGGAAAGATATATCCTAAAATAAAAAATACACGGAAGCATTCTGAGAAACTTCATTGTTTTGTGTGCATTCAACTCACAGAGTTGAACCTATCT;CE=1.9285GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV  0/1:-129.223,0,-44.7728:10000:PASS:0:110747:110747:2:0:0:19:59  0/1:-94.3442,0,-45.4931:10000:PASS:0:88163:88163:2:0:0:17:39 ```

creisle · 2021-04-28T21:51:58Z

ok so I actually might know what's going on here. It looks like the DELLY is using an alt format that is close but doesn't match the vcf 4.2 specification (despite the header)

r = reference base/seq
u = untemplated sequence/alternate sequence
p = chromosome:position

They have ]p] but we expect that to include sequences ]p]ur The alternate sequence can be empty but the reference sequence we don't consider optional. @calchoo can you double check the VCF 4.2 format for this make sure I'm interpreting it correctly

creisle · 2021-04-28T21:53:54Z

What version of delly are you using?

sarahdada · 2021-04-28T21:56:48Z

/gsc/software/linux-x86_64-centos7/delly-0.8.7/bin/delly is what i am using thanks cara!!

sarahdada · 2021-04-29T23:33:10Z

I used delly-0.8.1 , am clearly making an error here

                      MAVIS: 2.2.9
                      hostname: gphost14.bcgsc.ca
[2021-04-29 16:30:22] arguments
                        command = 'setup'
                        config = '/projects/pathMAVIS/file_both.cfg'
                        log = None
                        log_level = 'INFO'
                        output = '/projects/path/MAVIS'
                        skip_stage = []
Traceback (most recent call last):
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/util.py", line 65, in filepath
    file_list = bash_expands(path)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/util.py", line 158, in bash_expands
    raise FileNotFoundError('The expression does not match any files', expression)
FileNotFoundError: [Errno The expression does not match any files] None

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/sdada/miniconda3/bin/mavis", line 8, in <module>
    sys.exit(main())
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/main.py", line 482, in main
    config = _config.MavisConfig.read(args.config)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/config.py", line 379, in read
    return MavisConfig(**config_dict)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/config.py", line 264, in __init__
    raise err
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/config.py", line 257, in __init__
    self[sec] = validate_section(kwargs.pop(sec, {}), defaults, True)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/config.py", line 466, in validate_section
    value = cast_type(value)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/util.py", line 67, in filepath
    raise TypeError('File does not exist', path)
TypeError: Error in validating the reference section in the config. File does not exist None ```

creisle · 2021-04-30T17:32:14Z

TypeError: Error in validating the reference section in the config. File does not exist None ```

This sounds like you didn't add a reference file you need? or you set it to None. What does the reference section of your mavis config look like?

sarahdada · 2021-04-30T18:01:34Z

Hi Cara,

(Un)Shockingly you are right; I didnt have the right masking etc for my ref. Changed Ref. THANKS

sarahdada · 2021-04-30T18:13:55Z

Still looking like chrm 8. Really sorry if I'm messing up something w/delly
(base) [sdada@gphost14 MAVIS]$ mavis setup file.cfg -o /projects/path/MAVIS
                      MAVIS: 2.2.9
                      hostname: gphost14.bcgsc.ca
[2021-04-30 11:09:34] arguments
                        command = 'setup'
                        config = '/projects/path/MAVIS/file.cfg'
                        log = None
                        log_level = 'INFO'
                        output = '/projects/path/MAVIS'
                        skip_stage = []
                      creating output directory: '/projects/path/MAVIS/converted_inputs'
                      setting up the directory structure for PG0003838 as /projects/path/MAVIS/PG0003838_normal_genome
                      converting input command: ['convert_tool_output', '/projects/path/DELLY_0.8.1/patientcompared_dellysomatic_v81_hg38header.vcf', 'delly', False]
                      reading: /projects/path/DELLY_0.8.1/patientcompared_dellysomatic_v81_hg38header.vcf
Traceback (most recent call last):
  File "/home/sdada/miniconda3/bin/mavis", line 8, in <module>
    sys.exit(main())
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/main.py", line 600, in main
    raise err
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/main.py", line 582, in main
    pipeline = _pipeline.Pipeline.build(config)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/schedule/pipeline.py", line 350, in build
    libconf.inputs = run_conversion(config, libconf, conversion_dir)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/schedule/pipeline.py", line 81, in run_conversion
    convert_tool_output(
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/tools/__init__.py", line 34, in convert_tool_output
    _convert_tool_output(
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/tools/__init__.py", line 276, in _convert_tool_output
    rows = read_vcf(input_file, file_type, log)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 197, in convert_file
    raise err
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 194, in convert_file
    rows.extend(convert_record(vcf_record, log=log))
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 110, in convert_record
    chr2, end, orient1, orient2, ref, alt = parse_bnd_alt(alt)
  File "/home/sdada/miniconda3/lib/python3.8/site-packages/mavis/tools/vcf.py", line 74, in parse_bnd_alt
    raise NotImplementedError('alt specification in unexpected format', alt)
NotImplementedError: ('alt specification in unexpected format', ']chr8:43240816]') ```

sarahdada · 2021-04-30T18:57:07Z

 hello friends and fam

it seems like its an issue with my VCF (note bottom chr with 'N' in chromosome has a weird pattern and is missing a letter). going to re-bcf >vcf it, and if that wont work I am going to regenerate the delly bcf. the OTHER delly vcf works, which is a nice control. If none of this works i'll manually try and mess with it 

(base) [sdada@gphost14 DELLY_0.8.1]$ grep -B 10 'chr8:43240816' file_dellysomatic_v81_hg38header.vcf
chrUn_KI270336v1        2       BND00064084     A       [chrUn_KI270467v1:711[A .       PASS    IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrUn_KI270467v1;END=711;PE=11;MAPQ=23;CT=5to5;CIPOS=-51,51;CIEND=-51,51  GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-114.835,0,-264.594:10000:PASS:0:522:234:4:52:108:0:0       0/1:-120.162,0,-238.566:10000:PASS:0:1665:388:9:46:88:0:0
chrUn_KI270336v1        284     BND00064085     T       T]chrUn_KI270467v1:2612]        .       LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrUn_KI270467v1;END=2612;PE=2;MAPQ=24;CT=3to3;CIPOS=-395,395;CIEND=-395,395      GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-1000,-1000:10000:PASS:472:759:25470:0:6944:385:0:0       0/1:-1000,0,-1000:10000:PASS:1314:1830:29355:0:3639:1227:0:0
chrUn_KI270336v1        315     DEL00064086     A       <DEL>   .       LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrUn_KI270336v1;END=831;PE=2;MAPQ=6;CT=3to5;CIPOS=-215,215;CIEND=-215,215        GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-47.4989,-383.219:10000:PASS:497:297:1161:0:175:0:0:0     0/0:0,-56.4709,-532.986:10000:PASS:1529:451:1669:0:203:1:0:0
chrUn_KI270336v1        440     BND00064087     C       C]chrUn_KI270466v1:1097]        .       LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrUn_KI270466v1;END=1097;PE=3;MAPQ=21;CT=3to3;CIPOS=-50,50;CIEND=-50,50  GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-30.5308,0,-1000:10000:PASS:514:1810:4731:1:664:121:0:0     0/1:-796.708,0,-1000:10000:PASS:1586:3228:7851:1:1473:401:0:0
chrUn_KI270336v1        444     BND00064088     T       T]chrUn_KI270467v1:1485]        .       LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrUn_KI270467v1;END=1485;PE=2;MAPQ=21;CT=3to3;CIPOS=-50,50;CIEND=-50,50  GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-103.653,0,-399.956:10000:PASS:514:1821:1128:2:143:116:0:0  0/1:-536.932,0,-484.266:10000:PASS:1609:3349:2367:2:205:424:0:0
chrUn_KI270336v1        781     BND00064089     G       [chr3:93470364[G        .       LowQual PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr3;END=93470364;PE=0;MAPQ=0;CT=5to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=12;INSLEN=0;HOMLEN=4;SR=5;SRQ=0.952;CONSENSUS=TGATATTTTTTGTACAGTATAGAATATATACTTTGGGTATTTTGATATTTTATGTACAGTATACAATGTATGGTTTCTGAACTTTGATATTTCATGTAGAGTATAAAATATATATTTGGGGTACA;CE=1.73818 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   1/1:-1000,-199.238,0:10000:PASS:299:1496:158359:0:0:0:32:923    1/1:-1000,-65.3614,0:10000:PASS:568:2387:152387:0:0:0:19:346
chrUn_KI270336v1        861     BND00064090     T       T]chr3:93470801]        .       PASS    IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr3;END=93470801;PE=37;MAPQ=27;CT=3to3;CIPOS=-50,50;CIEND=-50,50 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-1000,0,-195.757:10000:PASS:447:1447:49:6:135:400:0:0       1/1:-1000,-524.548,0:10000:PASS:672:2094:54:6:175:3134:0:0
chrUn_KI270336v1        893     BND00064091     C       C[chr4:51107269[        .       LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr4;END=51107269;PE=4;MAPQ=23;CT=3to5;CIPOS=-469,469;CIEND=-469,469      GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-81.404,0,-261.164:10000:PASS:646:1446:8:4:137:137:0:0      0/1:-42.8954,0,-334.227:10000:PASS:847:2086:21:5:187:80:0:0
chrUn_KI270336v1        909     BND00064092     A       [chr3:93470362[A        .       LowQual PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr3;END=93470362;PE=0;MAPQ=0;CT=5to5;CIPOS=-9,9;CIEND=-9,9;SRMAPQ=9;INSLEN=0;HOMLEN=8;SR=95;SRQ=0.970414;CONSENSUS=TACAGTATAGAATATATACCTTGGGTACTTTGATATTTTATGTACAGTATATAATATATGGTTTGTGAACTTTGATATTTCATGTAGAGTATAAAATATATATTTGGGGTACATTGATATTATATGTACAGTATATAATCTATATTTGATGTACTTTCATATTTTATGT;CE=1.73195  GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   1/1:-1000,-1000,0:10000:PASS:849:1443:158359:0:0:0:521:12926    1/1:-1000,-1000,0:10000:PASS:991:2082:152386:0:0:0:423:7575
chrUn_KI270336v1        926     BND00064093     T       T]chr3:93470799]        .       PASS    PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr3;END=93470799;PE=0;MAPQ=0;CT=3to3;CIPOS=-13,13;CIEND=-13,13;SRMAPQ=32;INSLEN=0;HOMLEN=12;SR=5;SRQ=0.968504;CONSENSUS=AAATATAGATTATATACTGTACATAAAATATCAAAGTACCCCAATATATATTATATACTGTACATGAAATATCAAAGTTCACAAACTATATATTATGTACTGTACATAAAATATCAAAGTACCCA;CE=1.72472 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   1/1:-1000,-1000,0:10000:PASS:1211:1442:49:2:0:0:175:13374       1/1:-1000,-1000,0:10000:PASS:1225:2072:54:3:0:0:183:7818
chrUn_KI270337v1        2       BND00064094     N       ]chr8:43240816] .       LowQual PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr8;END=43240816;PE=0;MAPQ=0;CT=5to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=15;INSLEN=0;HOMLEN=1;SR=3;SRQ=1;CONSENSUS=ATTGTATACTGTACATAAAATATCAAAGTATCCAAAGTATGTATTATAAGCTGTAGATAAAATATCAAAGTACCCAAACTATATATTATATACTGTACATAAAATATGAAAGTACCCAAAGTAT;CE=1.76063      GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-755.564,0,-50.8002:10000:PASS:0:1700:167:20:0:0:64:298     0/1:-81.8446,0,-127.519:10000:PASS:0:5742:270:43:0:0:68:51 ```

creisle · 2021-04-30T19:17:07Z

ok, looks like this is an input issue rather than a bug so I am going to remove the bug label for now. If you are able to determine whether it is a problem with DELLY or BCFtools then you can reference this issue when you create one in the corresponding repo for the bug. In the meantime if we are

sarahdada added the bug label Apr 27, 2021

creisle added the SV caller Tickets related to support for inputs from different SV callers label Apr 28, 2021

creisle removed the bug label Apr 30, 2021

creisle closed this as completed Oct 29, 2021

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Error during MAVIS setup #246

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Error during MAVIS setup #246

Error during MAVIS setup #246

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