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GATK allele frequencies

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"

gatk allele frequency
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updated by vakul.mohanty vakul.mohanty • written by jyu429 jyu429

1 answer

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

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written by vakul.mohanty vakul.mohanty

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