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Fix #604 Update VEP 111.0 to 113.3 #682

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Fix #604 Update VEP 111.0 to 113.3 #682

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@dennishendriksen dennishendriksen commented Feb 3, 2025 •
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running tests ...
vcf/aip                                  | PASSED | 339915=completed test/output/vcf/aip/.nxf.log
vcf/chd7                                 | PASSED | 339916=completed test/output/vcf/chd7/.nxf.log
vcf/corner_cases                         | PASSED | 339917=completed test/output/vcf/corner_cases/.nxf.log
vcf/deb_register                         | PASSED | 339918=completed test/output/vcf/deb_register/.nxf.log
vcf/empty_input                          | PASSED | 339919=completed test/output/vcf/empty_input/.nxf.log
vcf/empty_output_filter_samples          | PASSED | 339920=completed test/output/vcf/empty_output_filter_samples/.nxf.log
vcf/empty_output_filter                  | PASSED | 339921=completed test/output/vcf/empty_output_filter/.nxf.log
vcf/filter_samples                       | PASSED | 339922=completed test/output/vcf/filter_samples/.nxf.log
vcf/liftover                             | KAPUTT | 339923=failed    test/output/vcf/liftover/.nxf.log
vcf/multiproject_classify                | PASSED | 339924=completed test/output/vcf/multiproject_classify/.nxf.log
vcf/mvid                                 | PASSED | 339925=completed test/output/vcf/mvid/.nxf.log
vcf/str                                  | KAPUTT | 339926=failed    test/output/vcf/str/.nxf.log
vcf/trio                                 | PASSED | 339927=completed test/output/vcf/trio/.nxf.log
vcf/vkgl_lb                              | PASSED | 339928=completed test/output/vcf/vkgl_lb/.nxf.log
vcf/vkgl_lp                              | FAILED | 339929=completed test/output/vcf/vkgl_lp/.nxf.log
vcf/vkgl_vus                             | PASSED | 339930=completed test/output/vcf/vkgl_vus/.nxf.log
done

vcf/vkgl_lp failure analysis

# result counts of aip, chd7, deb_register and mvid are equal
# vkgl_lb results have slightly improved
[umcg-dhendriksen@betabarrel bump_vep113]$ zcat ../v8.2.0/test/output/vcf/vkgl_lb/vip.vcf.gz | grep -vc "^#"
4528
[umcg-dhendriksen@betabarrel bump_vep113]$ zcat test/output/vcf/vkgl_lb/vip.vcf.gz | grep -vc "^#"
4523 <-- improvement of 5

# vkgl_lp results are slightly worse
$ zcat test/output/vcf/vkgl_lp/vip.vcf.gz | grep -vc "^#"
26706 <-- threshold >= 26732

$ zcat ../v8.2.0/test/output/vcf/vkgl_lp/vip.vcf.gz | grep -v "^#" | cut -f 1,2 > ~/vep111.txt
$ zcat test/output/vcf/vkgl_lp/vip.vcf.gz | grep -v "^#" | cut -f 1,2 > ~/vep113.txt
$ diff ~/vep111.txt ~/vep113.txt

1305d1304
< chr1  161170657
2011d2009
< chr1  244055169
2907d2904
< chr2  47806199
3139d3135
< chr2  108763256
3374d3369
< chr2  165370204
3503d3497
< chr2  166048943
3509d3502
< chr2  166052915
5211d5203
< chr3  38551394
5237d5228
< chr3  38585698
5244,5245d5234
< chr3  38587404
< chr3  38587413
5581d5569
< chr3  71001002
7782d7769
< chr5  177293891
8546d8532
< chr6  121447177
8549d8534
< chr6  121447263
10764d10748
< chr9  2060890
10767d10750
< chr9  2084101
10776,10777d10758
< chr9  2110398
< chr9  2115938
12033a12015
> chr10 68122244
14677d14658
< chr12 51806300
15427d15407
< chr12 121626949
17462d17441
< chr15 64400815
22621d22599
< chr19 10994969
24095d24072
< chr21 36937316
25547d25523
< chrX  70445554
25588,25589d25563
< chrX  71223734
< chrX  71223738

case 1: chr1 161170657

$ zcat ../v8.2.0/test/output/vcf/vkgl_lp/intermediates/vip_classifications.vcf.gz | grep 161170657
chr1    161170657       .       C       CATAGTGGCTGTGT  .       .       CSQ=ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_000309.5|protein_coding|11/13||NM_000309.5:c.1136_1137insATAGTGGCTGTGT|NP_000300.1:p.Ser380Ter|1330-1331/1672|1136-1137/1434|379/477|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.9688657|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_001014443.3|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001122764.3|protein_coding|11/13||NM_001122764.3:c.1136_1137insATAGTGGCTGTGT|NP_001116236.1:p.Ser380Ter|1391-1392/1733|1136-1137/1434|379/477|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1||1|EntrezGene||||||||||||||||||||||||||||VUS|0.9705777|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|B4GALT3|8703|Transcript|NM_001199873.1|protein_coding|||||||||||1|652|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|B4GALT3|8703|Transcript|NM_001199874.1|protein_coding|||||||||||1|652|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_001319847.2|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_001319848.2|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001350128.2|protein_coding|10/12||NM_001350128.2:c.1037_1038insATAGTGGCTGTGT|NP_001337057.1:p.Ser347Ter|1292-1293/1634|1037-1038/1335|346/444|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.9626447|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001350129.2|protein_coding|11/13||NM_001350129.2:c.728_729insATAGTGGCTGTGT|NP_001337058.1:p.Ser244Ter|1410-1411/1752|728-729/1026|243/341|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.66184825|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001350130.2|protein_coding|11/13||NM_001350130.2:c.650_651insATAGTGGCTGTGT|NP_001337059.1:p.Ser218Ter|1423-1424/1765|650-651/948|217/315|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.53904563|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001350131.2|protein_coding|10/12||NM_001350131.2:c.650_651insATAGTGGCTGTGT|NP_001337060.1:p.Ser218Ter|1248-1249/1590|650-651/948|217/315|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.704965|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001365398.1|protein_coding|11/13||NM_001365398.1:c.1136_1137insATAGTGGCTGTGT|NP_001352327.1:p.Ser380Ter|1246-1247/1588|1136-1137/1434|379/477|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.93542033|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001365399.1|protein_coding|10/12||NM_001365399.1:c.1025_1026insATAGTGGCTGTGT|NP_001352328.1:p.Ser343Ter|1280-1281/1622|1025-1026/1323|342/440|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.9576504|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001365400.1|protein_coding|10/12||NM_001365400.1:c.728_729insATAGTGGCTGTGT|NP_001352329.1:p.Ser244Ter|1233-1234/1575|728-729/1026|243/341|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.7415555|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|stop_gained&frameshift_variant|HIGH|PPOX|5498|Transcript|NM_001365401.1|protein_coding|10/12||NM_001365401.1:c.650_651insATAGTGGCTGTGT|NP_001352330.1:p.Ser218Ter|1214-1215/1556|650-651/948|217/315|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.8523693|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|B4GALT3|8703|Transcript|NM_003779.4|protein_coding|||||||||||1|652|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_012475.5|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb      GT      1/1

$ zcat test/output/vcf/vkgl_lp/intermediates/vip_classifications.vcf.gz | grep 161170657
chr1    161170657       .       C       CATAGTGGCTGTGT  .       .       CSQ=ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_000309.5|protein_coding|11/13||NM_000309.5:c.1136_1137insATAGTGGCTGTGT|NP_000300.1:p.Ala379_Ser380insTer|1330-1331/1672|1136-1137/1434|379/477|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0037666822|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_001014443.3|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001122764.3|protein_coding|11/13||NM_001122764.3:c.1136_1137insATAGTGGCTGTGT|NP_001116236.1:p.Ala379_Ser380insTer|1391-1392/1733|1136-1137/1434|379/477|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1||1|EntrezGene||||||||||||||||||||||||||||VUS|0.0041686427|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|B4GALT3|8703|Transcript|NM_001199873.1|protein_coding|||||||||||1|652|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|B4GALT3|8703|Transcript|NM_001199874.1|protein_coding|||||||||||1|652|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_001319847.2|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_001319848.2|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001350128.2|protein_coding|10/12||NM_001350128.2:c.1037_1038insATAGTGGCTGTGT|NP_001337057.1:p.Ala346_Ser347insTer|1292-1293/1634|1037-1038/1335|346/444|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0039777486|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001350129.2|protein_coding|11/13||NM_001350129.2:c.728_729insATAGTGGCTGTGT|NP_001337058.1:p.Ala243_Ser244insTer|1410-1411/1752|728-729/1026|243/341|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0008023577|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001350130.2|protein_coding|11/13||NM_001350130.2:c.650_651insATAGTGGCTGTGT|NP_001337059.1:p.Ala217_Ser218insTer|1423-1424/1765|650-651/948|217/315|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0006965187|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001350131.2|protein_coding|10/12||NM_001350131.2:c.650_651insATAGTGGCTGTGT|NP_001337060.1:p.Ala217_Ser218insTer|1248-1249/1590|650-651/948|217/315|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0007333684|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001365398.1|protein_coding|11/13||NM_001365398.1:c.1136_1137insATAGTGGCTGTGT|NP_001352327.1:p.Ala379_Ser380insTer|1246-1247/1588|1136-1137/1434|379/477|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0023535127|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001365399.1|protein_coding|10/12||NM_001365399.1:c.1025_1026insATAGTGGCTGTGT|NP_001352328.1:p.Ala342_Ser343insTer|1280-1281/1622|1025-1026/1323|342/440|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.003264196|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001365400.1|protein_coding|10/12||NM_001365400.1:c.728_729insATAGTGGCTGTGT|NP_001352329.1:p.Ala243_Ser244insTer|1233-1234/1575|728-729/1026|243/341|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.00078224664|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|inframe_insertion&stop_retained_variant|MODERATE|PPOX|5498|Transcript|NM_001365401.1|protein_coding|10/12||NM_001365401.1:c.650_651insATAGTGGCTGTGT|NP_001352330.1:p.Ala217_Ser218insTer|1214-1215/1556|650-651/948|217/315|A/A*WLCX|gct/gcATAGTGGCTGTGTt||1||1|||EntrezGene||||||||||||||||||||||||||||VUS|0.0016810425|||||||AD&AR||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|B4GALT3|8703|Transcript|NM_003779.4|protein_coding|||||||||||1|652|-1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,ATAGTGGCTGTGT|downstream_gene_variant|MODIFIER|USP21|27005|Transcript|NM_012475.5|protein_coding|||||||||||1|4934|1|||EntrezGene||||||||||||||||||||||||||||VUS|0.20895535|||||||||||||||||||||||||99.5061||0.069777|||||||LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb        GT      1/1

likely related to the issues reported in Ensembl/ensembl-vep#1710 and Ensembl/ensembl-vep#1796 that look to be fixed VEP v114 in Ensembl/ensembl-variation#1149.

case 2: chr1 244055169

$ zcat test/output/vcf/vkgl_lp/intermediates/vip_classifications.vcf.gz | grep 244055169
chr1    244055169       .       T       G       .       .       CSQ=G|missense_variant|MODERATE|ZBTB18|10472|Transcript|NM_001278196.2|protein_coding|2/2||NM_001278196.2:c.1368T>G|NP_001265125.1:p.His456Gln|1723/4030|1368/1569|456/522|H/Q|caT/caG||1||1|||EntrezGene|||||0|0.992||||||||||||24|1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.41383666||||||1|AD|||||||||||||||||0.832|99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,G|3_prime_UTR_variant|MODIFIER|ZBTB18|10472|Transcript|NM_001421566.1|protein_coding|3/3||NM_001421566.1:c.*572T>G||1432/3739||||||1||1|||EntrezGene|||||||||||||||||||1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.0005798336||||||1|AD||||||||||||||||||99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,G|missense_variant|MODERATE|ZBTB18|10472|Transcript|NM_006352.5|protein_coding|1/1||NM_006352.5:c.1368T>G|NP_006343.2:p.His456Gln|1675/3982|1368/1569|456/522|H/Q|caT/caG||1||1|||EntrezGene|||||0|0.992||||||||||||24|1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.38901222||||||1|AD|||||||||||||||||0.832|99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,G|missense_variant|MODERATE|ZBTB18|10472|Transcript|NM_205768.3|protein_coding|2/2||NM_205768.3:c.1395T>G|NP_991331.1:p.His465Gln|1544/3851|1395/1596|465/531|H/Q|caT/caG||1||1||1|EntrezGene|||||0|0.987||||||||||||24|1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.49117047||||||1|AD|||||||||||||||||0.832|99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb  GT      1/1
$ zcat ../v8.2.0/test/output/vcf/vkgl_lp/intermediates/vip_classifications.vcf.gz | grep 244055169
chr1    244055169       .       T       G       .       .       CSQ=G|missense_variant|MODERATE|ZBTB18|10472|Transcript|NM_001278196.2|protein_coding|2/2||NM_001278196.2:c.1368T>G|NP_001265125.1:p.His456Gln|1723/4030|1368/1569|456/522|H/Q|caT/caG||1||1|||EntrezGene|||||0|0.992||||||||||||24|1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.41383666||||||1|AD|||||||||||||||||0.832|99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb,G|missense_variant|MODERATE|ZBTB18|10472|Transcript|NM_006352.4|protein_coding|1/1||NM_006352.4:c.1368T>G|NP_006343.2:p.His456Gln|1965/4272|1368/1569|456/522|H/Q|caT/caG||1||1|||EntrezGene|||||0|0.992||||||||||||24|1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.5495035||||||1|AD|||||||||||||||||0.832|99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LP|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lp,G|missense_variant|MODERATE|ZBTB18|10472|Transcript|NM_205768.3|protein_coding|2/2||NM_205768.3:c.1395T>G|NP_991331.1:p.His465Gln|1544/3851|1395/1596|465/531|H/Q|caT/caG||1||1||1|EntrezGene|||||0|0.987||||||||||||24|1|25|41|6|0.00|0.00|0.00|0.00|ZBTB18|VUS|0.49117047||||||1|AD|||||||||||||||||0.832|99.2687|0.91219|0.599415||||0.776723572949214||-0.223000004887581|LB|filter&vkgl&clinVar&chrom&gene&gnomAD&gnomAD_AF&sv&spliceAI&utr5&capice&exit_lb        GT      1/1

NM_006352.4 updated to NM_006352.5 in VEP v113 resulting in a different CAPICE score.

case 3: chr2 47806199

same as case 1

case 4: chr2 108763256

NM_006267.5 had no PolyPhen score in VEP v111 but got a PolyPhen score of 0.301 in VEP v113 resulting in a different CAPICE classification.

According to the VEP documentation the PolyPhen version should be the same though:
https://github.com/Ensembl/public-plugins/blob/release/111/docs/htdocs/info/docs/tools/vep/script/vep_cache.html#L191
https://github.com/Ensembl/public-plugins/blob/release/113/docs/htdocs/info/docs/tools/vep/script/vep_cache.html#L191

case 5: chr2 165370204

same as case 4

case 6: chr2 166048943

same as case 4

case 7: chr2 166052915

same as case 4

case 8: chr3 38551394

same as case 4

case 9: chr3 38585698

same as case 4

case 10: chr3 38587404

same as case 4

case 11: chr3 38587413

same as case 4

case 12: chr3 71001002

same as case 1

case 13: chr5 177293891

same as case 1

case 14: chr6 121447177

same as case 4

case 15: chr6 121447263

same as case 4

@dennishendriksen dennishendriksen changed the title Update VEP 111.0 to 113.3 Fix #604 Update VEP 111.0 to 113.3 Feb 3, 2025
@dennishendriksen dennishendriksen mentioned this pull request Feb 4, 2025
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@dennishendriksen