Analyzing VCF file

Question

[Sakhaa]

Hello everyone,

I am working on WGS workflows and I am beginner in that

And I would like to know how can I rank false positive calls by depth in VCF file, which tool is useful to use and generate a plots?

[Sakhaa]

Thank you very much for you comment @Pierre Lindenbaum,

I have used the VRSQ, but how can I know or extract the FP only from vcf file, I need to Identify the number of alleles on each FP site, then Rank false positive calls by depth.

Answer 1

[Pierre Lindenbaum]

you could use https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php with -an DP

but it is a bad idea for exomes : https://software.broadinstitute.org/gatk/documentation/article?id=11084

Depth of coverage (the DP annotation invoked by Coverage) should not be used when working with exome datasets since there is extreme variation in the depth to which targets are captured. In whole genome experiments this variation is indicative of error but that is not the case in capture experiments.

[Sakhaa]

Thank you very much for you comment @Pierre Lindenbaum,

I have used the VRSQ, but how can I know or extract the FP only from vcf file, I need to Identify the number of alleles on each FP site, then Rank false positive calls by depth.

[igor]

There are a few suggestions here: Extracting this data frame from a .vcf file