Joint genotyping using GenotypeGVCFs command line

suggi_01suggi_01 germanyMember
edited July 2016 in Ask the GATK team

Dear all,
we have set up a bwa + gatk best pratices pipeline for variant calling on exome data. we use the haplotype caller
in gvcf mode. my question is how to set up the genotype gvcf module for multiple samples:

Example for 2 samples:
java -jar GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R reference.fasta \
--variant sample1.g.vcf \
--variant sample2.g.vcf \
-o output.vcf

But how can perform this for lets say 100 gvcfs?

For that I tried to put the gvcfs in a list row by row and tried following on the command line:

cat gvcfs.list | genotypegvcf.sh $folder {}

But this takes only each gvcf seperately and generates one vcf per gvcf but
cannot perform joint genotyping. Further I have tried to put the gcvfs in one row
one after another but that didn't work either.

Appreciate your help very much.

Best,
Sugi

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