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?
When you say "known/published form of RNA editing", do you have a VCF file already ? and just trying to get the counts for ALT/REF allele ?
What I meant by known/published is that we're not fishing for some kind of new variation, but quantifying a known/real variation. It is an addition of an A into a poly A repeat in the FAS transcript that affects function.
http://www.ncbi.nlm.nih.gov/pubmed/21793106
I have VCF files (the lines in the original post are from VCF files from two different samples), and yes I am trying to get counts for the ALT/REF allele. The problem is that for most samples, GATK doesn't annotate this (see the second VCF file line from the original post)