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Sorry,
raredisease pipeline works for `germline` or `somatic` mutations? Can be used when there is no normal sample available (`tumour only mode`)?
Is any restriction for depth of coverage?
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Hi, I am using smoove to call SVs.
I want to know why some mutations in the chromosome are INV and some are BND. There are some results, for example:
chr2 29225539 471_1 N N] CHR2: 42271404] 2064.…
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Let's use this issue to track example papers to use as references in class. Ideally this will include:
- authors from the FH community
- exhibit reproducible methods
- different model systems (huma…
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There are several research papers and webpages that can be helpful to the cognoma task. Maybe I missed it, but I am not aware of any other issue that addresses this question. It would be good to have…
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Hello!
Upon using SURVIVOR to merge 2 VCF files from the same caller, I've noticed that the `DR` field always report `0,0` despite the reads information being available in both the VCF files. What …
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Hello,
I ran this data set on filtered output from Mutect2 (tumor vs normal, single patient with PoN of 4 samples). I got the mutation list by querying the vcf file from bcftools so I get the colum…
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As a TL I would to check the report consistency, identify and flag inconsistencies so that we can improve confidence in the report.
**Acceptance Criteria**
- [ ] Identify report rows where the m…
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I am trying to apply CNVkit to detection of sCNAs (somatic copy number alternations) with clinical samples.
Now, as a test I am trying to detect the sCNAs in HCC1395 cell line. I performed copy numbe…
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Chris and Sangtae;
This is a follow-up to a bcbio discussion (https://github.com/chapmanb/bcbio-nextgen/issues/2112#issuecomment-338307641) which I thought could use it's own thread. In bcbio we're c…
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I've run into an error when attempting to run the Nextflow pipeline, so thought I'd reach out in case it's something you've encountered and can quickly identify what might be causing it. Some of the o…