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Trouble combining SNP and (hard filtered) indels vcfs for same samples
Using UG I have jointly called a vcf for about 830 subjects and am trying to filter it using VQSR. Because the data is targeted capture (and the caller is UG), I haven't had success using the mixture model approach for indels and instead used hard filters (mixture approach worked fine for SNPs). So, I now have nice filter-status annotated snp and indel vcf files and just want to combine them into a single vcf, but GATK throws an error. I am using the following syntax:
-T CombineVariants \ -V /home/UG_2456bams_833sub_all_filtered_indels.vcf \ -V /home/UG_2456bams_833sub_all_filtered_SNPs.vcf \ -o /home/UG_2456bams_833sub_all_fin.vcf \
And receiving the following error:
ERROR MESSAGE: Duplicate sample names were discovered but no genotypemergeoption was supplied. To combine samples without merging specify --genotypemergeoption UNIQUIFY. Merging duplicate samples without specified priority is unsupported, but can be achieved by specifying --genotypemergeoption UNSORTED.
I take it I should include a --genotypemergeoption argument? If so, which one? I ma a bit confused as to why this would be required as I am not really 'merging' genotypes, but rather appending them.