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HaplotypeCaller is reporting DP in HOMREF region differently when ploidy is set to 1 with different Interval inputs #8943
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@jamesemery will look into this later on in the week |
Also tested with 4.3.0.0 -- same result |
@jamesemery -- did you happen to get a change to look at this? |
Hi @cmatKhan Currently the only way to fix this issue for you is to enable I hope this helps. |
Sorry for the delayed response @cmatKhan. The fix here is a little complicated because its a confluence of expected behaviors adding up to this. Specifically in So far nothing seems to obviously be bugged (we don't test/use haploid calling mode very often so its less well tested and this sort of issue is not surprising). We might be over-confident about reporting We didn't identify a good fix for this issue on our end but you might as well know that we looked into it and have considered why you are seeing this behavior. |
Thank you for the explanation. For what it's worth, that matches very well with what I observed in the gvcf. I appreciate the better insight. I think it is worth putting a note to this effect in the |
Hi all.
This looks like an issue presented by a forum post
Haplotypecaller FORMAT:DP is affected by the interval in WGS
User uploaded a toy data for us to test and I was able to recreate this issue under GATK 4.6.0.0. I have not tested it with any other versions.
When whole contig is given as interval all variant sites in the multisample VCF is reported with DP value much less than what it is supposed to be in samples where no variation occur. Samples with variants are shown as expected DP. Setting ploidy 2 for this analysis restores the expected DP value for samples with HOMREF sites no matter what interval is used. Numbers can be seen in the figure as well as those variant contexts.
This is what user and I got with the whole contig given as interval
This is what comes when -L is set to
CP022325.1:69347-69349
. This is the same DP reported when ploidy is set to 2 no matter what interval is used. This is also the expected DP value.User data is in the incoming folder with name
cmateusiak_20240805.tar.gz
The reference genome is a fungal one from the below link
Fungi reference C.NeoformansKN99
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