HaplotypeCaller '--emitRefConfidence' gives same PL(0) to two genotypes
Posted in Ask the GATK team | Last updated on 2014-03-25 19:07:22

Comments (14)


In our downstream analysis we have to differentiate between non-variants because of no coverage and confident reference calls. Because of this, we need to pay close attention to HaplotypeCaller non-variant calls. Doing this we found calls like this one:

17 7127955 . G <NON_REF> . . END=7127955 GT:DP:GQ:MIN_DP:PL 0/0:29:0:29:0,0,468

Would it be possible to get a feeling why this initial call is giving the same PL(0) to 0/0 and 0/1. If you look at the alignment,after "Data Pre-processing" best practices, we can see there is strong evidence this is a 0/0 position.

GenotypeGVCFs won't call this position as variant, which is good.

Thanks, Carlos

PS: I tried to add a BAM file with the relevant region and I got "Uploaded file type is not allowed".

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