User: newbio17
newbio17 • 80
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Posts by newbio17
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... Hello all,
I was wondering if anyone has experience running Pisces and/or Octopus on whole-exome sequencing samples (100-200x) for somatic variant calling.
Eventually, I would like to compare the variants from Pisces/Octopus with those from Mutect2 (potentially a consensus approach involving all 3 ...
written 6 weeks ago by
newbio17 • 80
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... > did you actually look at the BAM files yourself
Yeah. I mentioned that I did this for handful of coding regions with no noticeable oddities.
> The reason you have poor overlap is because your true somatic variants are not being called in the matched analysis
I agree, but what I'm concerne ...
written 8 weeks ago by
newbio17 • 80
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Comment:
C: error en trimmomatic
... I think this previous biostar post might help you with the "Unknown trimmer" runtime exception: [https://www.biostars.org/p/239601/][1]
[1]: https://www.biostars.org/p/239601/ ...
written 8 weeks ago by
newbio17 • 80
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... > Just to clarify, you see variants in your tumor sample, but not in your normal sample, but they are not being called when you are using that matched normal.
Let me clarify what I was doing with the tumor-only approach. I first call somatic variants using Mutect2 on the tumor BAM file. Then I c ...
written 8 weeks ago by
newbio17 • 80
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... > Are you targeting non-coding regions?
I'm not specifically interested in non-coding regions, but I examined them since they showed up to make sure they weren't due to some alignment errors.
> Do the variants make sense in terms of where they are on your venn diagram? For example, do the un ...
written 10 weeks ago by
newbio17 • 80
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... Ah okay. I did briefly take a look at couple of files I tested, but nothing too out of ordinary. However, I only examined a couple cases such as intron variants in order to make sure the region was consistent with Agilent's target region. What do you recommend I look for specifically (aside from pot ...
written 10 weeks ago by
newbio17 • 80
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... Thank you for your comment.
I did see much fewer somatic variants when I ran the tumor-only pipeline for my samples before testing with the TCGA samples for troubleshooting. I'm not sure what you mean by misalignment. Do you mean to say that the .bam files might have been generated using different ...
written 11 weeks ago by
newbio17 • 80
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... Sorry, I didn't get the notifications for the comments. I ran a couple of other matched data and the overlap is still low (10-15%) between the two workflows.
For igor's second comment, I did try running the germline variant calling on the normal samples and tried to see if the germline variants ov ...
written 11 weeks ago by
newbio17 • 80
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... Discussion thread can be found [here][1]. A developer responded asking how I compiled panel of normals, but not much to go on off of yet.
[1]: https://gatk.broadinstitute.org/hc/en-us/community/posts/360057810051-Mutect2-somatic-variant-calling-with-without-matched-normal-sample ...
written 11 weeks ago by
newbio17 • 80
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... Have you tried posting on GATK forums? They updated the somatic calling when they went from GATK3 to GATK4 so they might not have a parameter similar to the one you mentioned. ...
written 11 weeks ago by
newbio17 • 80
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