Megan Shand
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Activity overview
Latest activity by Megan Shand-
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...
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Megan Shand commented,
Hello, I believe SplitNCigarReads should still be splitting reads, it just might be soft clipping instead of hard clipping the ends in GATK 4 vs 3. Do you see supplemental alignments for these read...
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Megan Shand commented,
Hi xianfeng xu, We haven't tried this pipeline on somatic samples ourselves, but if I were to take a first pass at calling somatic mitochondrial variants, I would run this pipeline separately on th...
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Megan Shand commented,
Hi Changhan, Did you use the mitochondria best practices WDL? If so, then I'm not surprised that there are no overlapping variants in the two VCFs. We only call the control region of the mitochondr...
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Megan Shand commented,
There have been some changes in that section of the code recently. Which version are you using?
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Megan Shand commented,
I think trimming adapters depends more on the sequencing methods than the fact that it is a fungal mitogenome. If you choose to skip that step I'd just be sure to look at your bams in IGV to make s...
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Megan Shand commented,
Sorry, I didn't see your last comment before I replied! If these samples don't have many variants, then you can still run BQSR, but without removing many known variant sites (since there aren't tha...
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Megan Shand commented,
Hi, I don't have any experience with fungal mitochondria samples, but I'll try to address what to look out for in choosing these tools. For the bootstrapping of BQSR, the key is that you want to ha...
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Megan Shand commented,
Matthew Dapas You're correct. In the current version of the pipeline we only use the shifted VCF for the control region, so your easy fix sounds very reasonable to me.