I am working with RNAseq data to look at a known/published form of RNA editing in a certain gene. I am using GATK (and their suggested pipeline for RNAseq data) and the DepthPerAlleleBySample annotation to measure the relative quantity of the wt and edited versions of the transcripts. For some samples, GATK makes the SNP call and correctly gives me reads per "allele" (in bold) like so:
chr10 90774093 . C CA,<NON_REF> 21.76 . BaseQRankSum=-0.006;DP=94;MLEAC=1,0;MLEAF=0.500,0.00;MQ=50.00;MQ0=0;MQRankSum=0.397;ReadPosRankSum=0.348 GT:AD:GQ:PL:SB 0/1:72,13,0:59:59,0,1657,276,1696,1972:47,25,7,6
However for most of my samples, it indicates the presence of a variant but makes no call.
chr10 90774093 . C <NON_REF> . . END=90774093 GT:DP:GQ:MIN_DP:PL 0/0:50:12:50:0,12,1432
I've checked the BAMs in IGV and the RNA edited reads are there. I'm not sure why its doing this, but I think that its due to the low number of RNA edited reads in some samples (e.g. 4 out of 55 in one sample with no call).
Is there a way to get IGV to make a SNP call even with a single variant read?