Hi All,

I am trying to subset a GVCF with multiple samples to a GVCF with smaller number of samples and I am not getting the results as expected.

First command used

gatk SelectVariants --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' -R Homo_sapiens_assembly38.fasta --variant combined.g.vcf --sample-name subset_samples.txt -O subset_combined.g.vcf

And the error received was:. Even though all the samples listed in the file subset_samples.txt are present in the input VCF

   A USER ERROR has occurred: Bad input: Samples entered on command line (through -sf or -sn) that are not present in the VCF
   A list of these samples: subset_samples.txt

    To ignore these samples, run with --allow-nonoverlapping-command-line-samples

Second command used:

gatk SelectVariants --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' -R Homo_sapiens_assembly38.fasta --variant combined.g.vcf --sample-name subset_amples.txt -O subset_combined.g.vcf--allow-nonoverlapping-command-line-samples

And the issue:

The output VCF still has all sample names

I am not sure, what I am missing in the commands to get the right output