Open
Conversation
Phased variants is read from vcf file by finding "1|0" or "0|1" substring in each vcf records. This should be done only to the last column. This fix still assumes input is a single sample vcf.
Collaborator
|
Thank you for catching this bug. If you have tested the modified code I can merge the PR. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Hi,
Phased variants is read from vcf file by finding "1|0" or "0|1" substring in each vcf records. This should be done only to the last column of a vcf record (in single sample vcf files), not the whole record. Similar for replacing the phasing.
Example: The following line is from a epi2me-labs/wf-human-variation + hapcut2 v1.3.1 run on this bam. The variant is unphased but line has a "0|1", which crashes the run by calling int() on a string:
chr6 145913508 . G A 25.38 PASS P;ANN=A|synonymous_variant|LOW|S HPRH|SHPRH|transcript|XM_017010691.2|protein_coding|24/30|c.4296C>T|p.Cys1432Cys|4457/5527|4296/ 5235|1432/1744||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcript|XM_006715439.4|protein_coding|2 4/31|c.4296C>T|p.Cys1432Cys|4457/11423|4296/5124|1432/1707||,A|synonymous_variant|LOW|SHPRH|SHPR H|transcript|XM_006715443.4|protein_coding|24/26|c.4296C>T|p.Cys1432Cys|4457/4780|4296/4524|1432 /1507||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcript|XM_017010693.2|protein_coding|24/31|c.42 96C>T|p.Cys1432Cys|4457/5304|4296/5073|1432/1690||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcri pt|XM_017010696.2|protein_coding|25/31|c.2853C>T|p.Cys951Cys|4074/5145|2853/3792|951/1263||,A|sy nonymous_variant|LOW|SHPRH|SHPRH|transcript|XM_024446394.1|protein_coding|25/31|c.2853C>T|p.Cys9 51Cys|4374/5445|2853/3792|951/1263||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcript|XM_01701069 2.1|protein_coding|24/30|c.4296C>T|p.Cys1432Cys|4695/5765|4296/5235|1432/1744||,A|synonymous_var iant|LOW|SHPRH|SHPRH|transcript|XM_024446393.1|protein_coding|25/31|c.3354C>T|p.Cys1118Cys|4590/ 5660|3354/4293|1118/1430||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcript|XM_011535719.3|protei n_coding|24/30|c.4296C>T|p.Cys1432Cys|4457/7072|4296/5034|1432/1677||,A|synonymous_variant|LOW|S HPRH|SHPRH|transcript|NM_001042683.3|protein_coding|24/30|c.4296C>T|p.Cys1432Cys|4956/7596|4296/ 5052|1432/1683||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcript|NM_001370327.1|protein_coding|2 4/30|c.4296C>T|p.Cys1432Cys|4530/7170|4296/5052|1432/1683||,A|synonymous_variant|LOW|SHPRH|SHPRH |transcript|NM_001370328.1|protein_coding|26/32|c.2853C>T|p.Cys951Cys|4114/6754|2853/3609|951/12 02||,A|synonymous_variant|LOW|SHPRH|SHPRH|transcript|NM_173082.4|protein_coding|24/30|c.4308C>T| p.Cys1436Cys|4968/7261|4308/4980|1436/1659||,A|downstream_gene_variant|MODIFIER|SHPRH|SHPRH|tran script|XR_002956273.1|pseudogene||n.*4666C>T|||||4666|,A|non_coding_transcript_exon_variant|MODI FIER|SHPRH|SHPRH|transcript|XR_942391.3|pseudogene|24/29|n.4457C>T||||||,A|non_coding_transcript _exon_variant|MODIFIER|SHPRH|SHPRH|transcript|XR_942393.3|pseudogene|24/29|n.4457C>T||||||,A|non _coding_transcript_exon_variant|MODIFIER|SHPRH|SHPRH|transcript|XR_942392.3|pseudogene|24/29|n.4 457C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|SHPRH|SHPRH|transcript|XR_942390.3|ps eudogene|24/29|n.4457C>T|||||| GT:GQ:DP:AD:AF:PS 1/1:25:89:0,86:0.9663:.Thanks!