Question: GATK allele frequencies
0
gravatar for jyu429
2.5 years ago by
jyu429120
United States
jyu429120 wrote:

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"

allele frequency gatk • 808 views
ADD COMMENTlink modified 2.5 years ago by vakul.mohanty240 • written 2.5 years ago by jyu429120
0
gravatar for vakul.mohanty
2.5 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

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

ADD COMMENTlink written 2.5 years ago by vakul.mohanty240
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