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AD field formatting errors
Hi. I have variants where the AD field is incorrectly formatted, such as
for a MULTI-allelic SNP.
The AD field should be 21,0,19 in this case.
I've been using GenotypeGVCFs in version:
nightly-2014-06-07-g1006061, Compiled 2014/06/07 00:01:21
using the HC incremental discovery pipeline.
I know that problems with the AD field in this pipeline are known; Is there any ETA for correcting it? It's making downstream analysis with our scripts very difficult. Should I try the latest nightly build?
I've previously seen problems with BIALLELIC SNPs having AD output such as 32,0,15 instead of 32,15 (which also threw off our scripts), but I am so far not seeing that with the 2014/06/07 nightly build. So at least the AD problem is partially corrected as far as I know.