GATK allele frequencies

Question

[jyu429]

Hi,

I'm using the GATK Haplotype caller to call for variants, but I'd like to output the genotype fields. For this, I believe I have to use the -GF option, but is this an incorrect way?

java -jar $HOME/Tools/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -GF -T HaplotypeCaller -R "imgt_VH_filtered.fasta" -I $PREFIX"realigned_bams/"$INDIVIDUALS_NAME"_realigned.bam" -ploidy 2 -stand_call_conf 30 -stand_emit_conf 10 -o $PREFIX"raw_vcfs/"$INDIVIDUALS_NAME"_raw.vcf"

Answer 1

[vakul.mohanty]

I think you will have to carry out joint genotyping to obtain genotype calls.