Megan Shand
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Activity overview
Latest activity by Megan Shand-
Megan Shand commented,
Hello, thanks for reporting this! I think it may be a bug. I'm working on a fix and will let you know once the code has been updated.
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Megan Shand commented,
Hi Michelle Lian, Both of these "extra args" arguments are used to add flexibility to the WDL. They are kind of a catch all string so that if someone would like to run this pipeline but they want t...
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Megan Shand commented,
Hi Alan Foley, The knownVcfs input here is only used in the BaseQualityScoreRecalibrator to mask out the sites with known variation. This is because that tools assumes that any mismatch base from t...
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Megan Shand commented,
Hi behzad, You should be able to use the VCF file you have from WES data in this tool. There is no specific reason that the input VCF file is called sites.vcf.gz in the documentation. I think it's ...
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Megan Shand commented,
Yes that's right (using the shifted_by_8000_bases.fasta). You should use those two interval lists when variant calling (one on the shifted version and one on the regular version) so that you only c...
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Megan Shand commented,
From glancing through the logs, it looks good! If you have a VCF that looks reasonable, that's a really good start too. One point I should make is that we do this whole alignment to the shifted ref...
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Megan Shand commented,
That interval list looks good! So hopefully those arguments to PrintReads will at least ensure that the bam you're using is valid (no missing mates). So part of the mitochondria pipeline is to rea...
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Megan Shand commented,
Hello, I have a couple of questions about this input data. Are you using gs://fc-ccb0e231-7c8d-4a45-82a3-0f3584a216c0/40c2c7c9-3d17-40b0-96e6-4b43d2b56250/MitochondriaPipeline/56b9e8ed-898c-4747-b8...
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Megan Shand commented,
Ah gotcha, great. For what it's worth, HaplotypeCaller does look at supplementary reads. If you're using a different caller it would definitely be a good idea to make sure that supplementary reads ...
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Megan Shand commented,
Ah, thank you I didn't understand the issue, but I think I see what you're saying now. I'm not sure exactly why this would have changed, but can I ask you to provide the cigar strings for that read...