Megan Shand
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Activity overview
Latest activity by Megan Shand-
Megan Shand commented,
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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Megan Shand commented,
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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Megan Shand commented,
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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Megan Shand commented,
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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Megan Shand commented,
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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Megan Shand commented,
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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Megan Shand commented,
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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Megan Shand commented,
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...
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Megan Shand commented,
Thanks for sharing your input data. I have discovered that in our pipeline the RAW_GT_COUNT annotation is added in the ReblockGVCFs step. This step is called here in our single sample pipeline. The...
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Megan Shand commented,
Thank you I will take a look!