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How to generate RO ad AO counts in vcf file to calculate altered allele frequency.
I'm want to calculate Alternate Allele Frequency from the vcf file. I came to know that it can be calculated based on RO(Reference allele observation count) and AO(Alternate allele observation count) fields. But these fields are missing in the vcf generated from samtools mpileup-bcftools(version 1.0) as well as GATK.
I tried -t, --output-tags argument from mpileup and got the error as :
Could not parse "AO" similarly for RO. I'm also interested if any parameter needs to be enabled to get AO and RO in unifiedgenotyper( v1.3-14-g348f2db) unfortunately I cannot upgrade to GATK version.
I tried -t, --output-tags argument from mpileup and got the error as :
Could not parse "AO" similarly for RO. I'm also interested if any parameter needs to be enabled to get AO and RO in unifiedgenotyper( v1.3-14-g348f2db) unfortunately I cannot upgrade to GATK version.