Hello,
I am trying to compare two VCFs: one generated by FreeBayes (multi-sample) and one by GATK (multi-sample generated by Genotype GVCFs). Before I compare the two I need to filter both, and I'm having trouble figuring out which INFO fields are in common between the two VCFs.
Below are the FreeBayes fields I would like to mimic in my filtering of the GATK VCF. Could you let me know what the equivalent field would be for GATK, if there is one at all?
AO - Count of full observations of this alternate haplotype
SAF/SAR - Number of alternate observations on the forward/reverse strand
RPR/RPL - Reads Placed Right/Left: number of reads supporting the alternate balanced to the right (3') (or left, 5') of the alternate allele
Thanks!