GATK BaseQualityRecalibrator

Question

[ayeraselvan]

Hi, I want to perform the base quality recalibration for a pool sequence data of population of flies. I have the vcf file with the variants for all the samples used. How to use this information for calling gatk BaseCalibrator. Should I use some hard filtering variants to use for BQSR process? How to determine the known variants from this?

Answer 1

[LChart]

The variant information is only used to mask polymorphic sites so that true mutations do not deflate quality scores. Just pass in your VCF instead of the dbSNP sites VCF. You want to ensure that the variants present are truly polymorphic, so filtering to variants seen multiple times, or that don't validate Hardy-Weinberg, would be a good idea.

[ayeraselvan]

I will proceed on with BQSR with the whole vcf file without any filtration. Thank you!