
Megan Shand
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Recent activity by Megan Shand Sort by recent activity-
I don't think it will make a substantial difference for the mitochondria workflow between those two interval lists, but we currently use the wgs_coverage_regions.hg38.interval_list with CollectWgsM...
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Hi Rich Roberts, SplitNCigarReads should only be used for variant calling. HaplotypeCaller should be looking at supplementary reads so the read depth should be unaffected. You will want to run Hapl...
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Unfortunately a reference sample is required. Ideally we would move away from this requirement, but the work is not prioritized at the moment since the thought was that a reference sample could be ...
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Following up here that the docker is now public here: us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:UG_vc_0.8.1_399932 This is a newer version that includes a bug fix and also note that the ou...
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Great that you were able to get through some portions of the pipeline! That docker being private is definitely unintentional. I'll make a ticket in the WARP repo and look into that.
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When you run ReblockGVCFs you should also include these arguments: "--annotations-to-keep TREE_SCORE --annotations-to-keep ASSEMBLED_HAPS --annotations-to-keep FILTERED_HAPS" in order to keep those...
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Perfect, that should fix it. I now see what made ReblockGVCFs so slow, so I'm going to add an error message when the input doesn't contain TREE_SCORE but that tree-score cutoff argument is used. Th...
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Ah, so I can confirm that we do run with the tree_score_cutoff argument. But, since you mentioned this, I did notice that you don't have the TREE_SCORE annotation in the gVCFs that you sent earlier...
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Hmm, that is definitely not expected. When we run on typical gVCFs with ~90M records it takes about 30 minutes. Did you notice any other tasks that seemed particularly slow? What kind of environmen...
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I'm not sure why chrX would be excluded, but I think fixing the sequencing dictionaries to match is the first step. If the tool runs to completion without an error and you're still not getting outp...