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I am trying to merge two vcfs (SNVs and INDELs) from the same sample. The problem appears to be that the INDEL vcf defines "combined_sample_name" but the SNV vcf does not. So when I merge I get two sample columns. How can I force GATK to treat them as a single sample?

I tried --assumeIdenticalSamples to do a "simple merge," but that made no difference.

As a side note, these vcfs are from an Ion Torrent machine.

Thanks!

java -jar $GATK \
    -R $TSP_FILEPATH_GENOME_FASTA \
    -T CombineVariants \
    --assumeIdenticalSamples \
    -V:${baseFolderName} ${i}/SNP_variants.vcf \
    -V:${baseFolderName} ${i}/indel_variants.vcf \
    -o ${RESULTS_DIR}/${baseFolderName}_variants.vcf

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