Merge multiple vcf files while preserving FILTER information

Question

[mkulecka]

Hello, I have multiple vcf files from different samples. I would like to combine all of the in one file but I would like to preserve information from FILTER field. For example if I have a vcf record which passes the filter in one sample:

chr1 949654 . A G 571.55 PASS

and fails it another

chr1 949654 . A G 571.55 FAILED

I would like a record in vcf file to be something like that

chr1 949654 . A G 571.55 PASS;FAILED

I already tried vcf-merge from http://vcftools.sourceforge.net/ - it just seems to ignore records without the PASS tag and there doesn't seem to be any option to turn that off. I also think that GATK CombineVariants won't do the trick; there's an option to include filtered-out variants but without including all the information from tags.

Answer 1

[Ram]

bcftools merge's -F should be useful here. https://samtools.github.io/bcftools/bcftools.html

I've seen that bcftools and vcftools together can address almost any need we may have with VCF files.

[mkulecka]

Unfortunately it doesn't preserve information on all filters - it can mark variant only as PASS or FAILED but not both, if ti passes a filter in one sample but not the other.