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ellisrichardj / BovTB-nf

Nextflow script for processing WGS data
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VCF2Consensus process fails for some samples #9

Closed ellisrichardj closed 4 years ago

ellisrichardj commented 5 years ago

Error code suggests that its linked to an issue in bcftools where two variants are overlapping. See https://github.com/samtools/bcftools/issues/888. Fix available in latest bcftools commit, but not yet in a full release.

ellisrichardj commented 5 years ago

This issue appears to have been resolved following the update of the pipeline to use the most recent version of the AF2122 reference genome. Monitor and close if no more issues

ellisrichardj commented 5 years ago

No further issues after updating to newest reference genome

ellisrichardj commented 5 years ago

Issues are still there in some cases - look at alternate method for calling consensus (or wait for fix in next bcftools release)

ellisrichardj commented 5 years ago

@Viloleal suggests normalizing and/or filtering BCF before calling consensus might be required

ellisrichardj commented 5 years ago

Normalizing and filtering fixed the error for some cases, but it still failed for others. As indicated in samtools/bcftools#888 and samtools/bcftools#938, installing the latest commit of bcftools (http://samtools.github.io/bcftools/howtos/install.html) does fix the issue, but the fix is not yet available in a versioned release. Suggest installing the latest commit and making sure the correct version is called from the nextflow script.

ellisrichardj commented 4 years ago

BCFtools recent release now includes this fix. Now need to test and implement v1.10 release

ellisrichardj commented 4 years ago

bcftools v1.10.2 fixes the issue and is used by default - no further problems