Question: GATK: SNP calls for variants with a single read to detect RNA editing
gravatar for tptacek3050
3.3 years ago by
United States
tptacek305060 wrote:

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?

rna editing rna-seq gatk • 1.4k views
ADD COMMENTlink modified 3.2 years ago by geek_y9.4k • written 3.3 years ago by tptacek305060

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 ?

ADD REPLYlink written 3.3 years ago by geek_y9.4k

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.


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)

ADD REPLYlink written 3.3 years ago by tptacek305060
gravatar for geek_y
3.2 years ago by
geek_y9.4k wrote:

GATK has a new tool called ASEReadcounter, which counts the number of bases for REF, ALT and others, but the link seems to be down right now. Otherwise, it should be easy to count the ALT and REF reads with pysam using a VCF and a BAM file.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by geek_y9.4k
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