Filter by variant type - Githubissues

jts / sga

de novo sequence assembler using string graphs

http://genome.cshlp.org/content/22/3/549

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Filter by variant type #104

Closed ljdursi closed 8 years ago

ljdursi commented 8 years ago

These commits:

Add a new VCFClassification, VCF_STRUCTURAL
Add a new option to somatic-variant-filters, --variant-type=STR, which can be ALL/SNV/INDEL/SV, with default ALL
Have somatic-variant-filters simply pass the VCF record to stdout if the variant type of the record is not that passed in --variant-type, otherwise performs the filtering/annotating as before.

I'm not sure if this is the best way to handle the command line options or not.

ljdursi commented 8 years ago

Better? Will bcftools norm decompose a complex substitution into a deletion + insertion? I don't want the annotation pipeline to miss any "indel" calls even if they're COMPLEX by this definition.

jts commented 8 years ago

I don't think we can rely on bcftools to break up complex calls like that. If you want them annotated with indels you'll have to change the if statement

ljdursi commented 8 years ago

Ok, so this version allows --variant-type=INDEL,COMPLEX