👨🔬 Beta Workflow to Modify Ploidy #145
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migbro
added
enhancement
| - region: Specific region to pull, in format 'chr21' or 'chr3:1-1000' | ||
| - dbsnp_vcf: dbSNP vcf file | ||
| - dbsnp_idx: dbSNP vcf index file | ||
| - contamination: Precalculated contamination value. Providing the value here | ||
| will skip the run of VerifyBAMID and use the provided value as ground truth. | ||
| - contamination_sites_bed: .Bed file for markers used in this | ||
| analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele) | ||
| - contamination_sites_mu: .mu matrix file of genotype matrix | ||
| - contamination_sites_ud: .UD matrix file from SVD result of genotype matrix | ||
| - re_calling_interval_list: Interval list to re-call | ||
| - wgs_evaluation_interval_list: Target intervals to restrict GVCF metric | ||
| analysis (for VariantCallingMetrics) | ||
| - sample_ploidy: If sample/interval is expected to not have ploidy=2, enter expected ploidy |
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Can you just put a blurb at the top that highlights:
regionre_calling_interval_listsample_ploidy
These are the three "active" inputs. It would be good to have an example like:
If you would like to recall trisomy 21, you would have:
- region = chr21
- sample_ploidy = 3
- re_calling_interval_list = the regions of chr21 that are expected to be ploidy = 3
tools/bedtools_intersect.cwl
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| - position: 2 | ||
| shellQuote: false | ||
| valueFrom: >- | ||
| -wa -header | bgzip -c -@ 4 > $(inputs.output_basename).bed_intersect.vcf.gz |
tools/samtools_cram_to_bam.cwl
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| input_cram: { type: File, secondaryFiles: ['.crai?'], doc: "cram file to convert", | ||
| inputBinding: { position: 2 } } | ||
| region: { type: 'string?', doc: "Specific region to pull, in format 'chr21' or 'chr3:1-1000'", | ||
| inputBinding: { position: 2 } } |
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Doesn't this positionally have to come after input_cram?
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technically it does, because the tie breaker of them both being position 2 is that I declared input cram first. However, that is a dangerous technicality, so I'll make it 1
Co-authored-by: Dan Miller <[email protected]>
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@dmiller15 , ok, made a tool to address the header issue. Runs pretty quick: https://cavatica.sbgenomics.com/u/d3b-bixu/kf-germline-harmonization-dev/tasks/be613e5e-34e4-4590-816e-375afc43b266/ |
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Implemented and modified @dmiller15 suggestion. Test here: https://cavatica.sbgenomics.com/u/d3b-bixu/kf-germline-harmonization-dev/tasks/45766bae-9c4f-462f-8c3a-13fb0644ae46/ |
🔧 better set secondaryfiles to accurately reflect requirements
Description
This started out as a research question for trisomy 21 in which we ran a version of this workflow for a collaborator to review. Since then, another collaborator has brought up a more general case of treating chr X as haploid when the sample is from a male. We achieve this by:
Fixes # https://d3b.atlassian.net/browse/BIXU-3785
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: