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VariantsToTable is not outputting all variants


I am using GATK4, I am not entirely following best practices in that I am combining RNAseq data in genotype gvcfs, doing variant filtering and extracting SNPs, then outputting a table (and the best practices for RNAseq is not fully developed.)

I am working with a cohort.g.vcf file with 47 samples. However, VariantsToTable only outputs 24 of them. I combined two sample sets by running genotype gvcfs to get a cohort gvcf, subjecting it to filtering, and then it seems my variants are all recognized in the header of my g.vcf files up until I get the .table output file from VariantsToTable. For whatever reason, VariantsToTable will output a table with only 24 samples included. I have never had this problem before when using the same pipeline. I tried the tag --showFiltered, thinking maybe there was some issue with filtration, but no luck.

My only guess is it is a problem originating all the way back from the headers generated by add read replace groups earlier in my pipeline, but I have no idea how that is even possible, unless, having too similar of input file names at that point in the pipeline caused add read replace groups to output the same ID's for different files, though, the pattern that VariantsToTable seems to follow seems random, and not related to an ID problem originating in the bam file headers. I have no clue how this could be possible, but maybe?

Has anyone else had this happen? Thanks so much.

Best Answer


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