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CombineGVCFs incorrectly parses last GVCF block consisting of HLA contig #4572
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I will assign to @droazen to delegate. |
@cmnbroad Could you have a look at this one when you get a chance? |
Original post on forum: https://gatkforums.broadinstitute.org/gatk/discussion/comment/47226#Comment_47226 |
@sooheelee I can see the original forum post, but I get a 404 when I click on the link at the top of this ticket (https://github.com/broadinstitute/dsde-docs/issues/3026). |
We need to ask @vdauwera to give you permission to view the dsde-docs repo. |
In the meanwhile, I've SLACKed you the location of the data @cmnbroad. |
Thanks @sooheelee. The code is definitely not correctly reconciling the accumulated variants/blocks that are remaining when traversal ends. I have a fix that resolves it, at least for this case, but this needs some more analysis and I'm going to have to write some additional tests to be sure that its correct. |
Great to hear there is a fix so soon @cmnbroad. Let me know if I can help out with creating test data. |
Data is sensitive and bug is recapitulated in https://github.com/broadinstitute/dsde-docs/issues/3026.
CombineGVCFs gives the following error message:
Here are the dictionary lines for two consecutive HLA-DRB1 contigs:
Notice the
LN
lengths match up. It appears that our tool is mistaking contig information.Note that
HLA-DRB1*16:02:01
is the very last contig in GRCh38.The text was updated successfully, but these errors were encountered: