Closed ghost closed 4 years ago
There are some complex situations where that can happen legitimately (discussed on Reading GLnexus pVCFs), however this doesn't appear to be one of them based on the information provided. The RNC field "MM" (M for Missing) is the genotyper claiming it did not see the first record at all. Is this an isolated discrepancy or is the sample exhibiting more general problems? Any overlapping gVCF records or anything otherwise unusual in the vicinity?
yes it was more general ... However your comment about "Missing" made me wonder if I could reproduce it, and I can't. I deleted the pVCF and generated it again. And this time, no problem.
I have no idea of what happened, but apparently something went wrong during the first run.
Hello,
I have a case where at some position a reference sample has the GT 0/1
And 1/1 in another sample
However, in the pVCF
The genotype of the first sample has moved from 0/1 to ./.
Is it an intended feature?
Thank you