I am using GATK beta 4.3 (downloaded yesterday) on trio whole-exome data, following best practices on germline SNP/indel calling up to HaplotypeCaller. I was unable to follow the example command in GenotypeGVCFs tool documentation "Perform joint genotyping on a set of GVCFs listed in a text file, one per line":
gatk-launch GenotypeGVCFs -R ~/hg38/Homo_sapiens_assembly38.fasta -V input_gvcfs.list -O trio11.vcf
It exited with this error:
[August 11, 2017 2:27:38 PM HKT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1495793664
***********************************************************************
A USER ERROR has occurred: Cannot read input_gvcfs.list because no suitable codecs found
My input_gvcfs.list looks like this:
F11.g.vcf
M11.g.vcf
P11.g.vcf
I have also tried listing the VCFs one by one, following the example command "Perform joint genotyping on a set of GVCFs enumerated in the command line":
gatk-launch GenotypeGVCFs -R ~/hg38/Homo_sapiens_assembly38.fasta -V F11.g.vcf -V M11.g.vcf -V P11.g.vcf -O trio11.vcf
But it exited with this error:
A USER ERROR has occurred: Argument '[V, variant]' cannot be specified more than once.
Please help! Thank you very much.
-Jamie