Entering edit mode
8.0 years ago
jyu429
▴
120
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"