User: vctrm67

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vctrm6720
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Posts by vctrm67

<prev • 116 results • page 1 of 12 • next >
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Extract VCF of tumor variants from a list of SNPs
... I have a list of germline SNPs. I want to get the read level information, etc. of these SNPs in the tumor BAM file and format it into a VCF (ie. to see the read level support for the germline SNPs in the tumor sample). Is there an easy way to do this? ...
snp mutect2 written 6 days ago by vctrm6720
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Getting sample IDs from dbGaP SRR?
... Does anyone know how to get the actual sample IDs from downloaded and extracted SRA files? Right now they are in the form "SRR..._dbGaP" but this doesn't help since this name isn't listed in the manifest. ...
dbgap written 6 days ago by vctrm6720
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Comment: C: CNVKit for unmatched tumor-only WGS samples
... I looked at that, but you can see that they use the `-n` tag, whereas I do not have any normals. I need to use the `-r` tag: ``` -r REFERENCE, --reference REFERENCE Copy number reference file (.cnn). ``` However, I cannot seem to generate a `.cnn` file without a target/a ...
written 19 days ago by vctrm6720
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Comment: C: CNVKit for unmatched tumor-only WGS samples
... Yes. There is no mention of what to do for this specific case. ...
written 20 days ago by vctrm6720
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CNVKit for unmatched tumor-only WGS samples
... Does anyone know how to use cnvkit on tumor-only WGS samples? I tried making a flat reference using b37 but I cannot without a target/antitarget bed file, which I don't have for an entire genome. ...
cnvkit written 20 days ago by vctrm6720
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Mutect2 missing mutations
... I am using the latest version of Mutect2 (4.1.9.0) and trying to call mutations from Mutect. I noticed that Mutect is not calling muations with clear read support in IGV. I tried some suggestions found on this forum [like this](https://gatk.broadinstitute.org/hc/en-us/community/posts/360059696811-Mu ...
mutect written 7 weeks ago by vctrm6720 • updated 7 weeks ago by _r_am32k
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SV calling with duplication amplification
... Based on diagrams like [this][1], it seems structural variant calling relies on detecting duplications based on if they lie in the same DNA strand. Can SV callers detect local duplications if the duplication is off the strand (ie. free-floating), like cytosolic focal amplifications? In this case the ...
sv written 3 months ago by vctrm6720
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Comment: C: Interpreting GISTIC2 output
... I would ask but they are not very responsive. ...
written 3 months ago by vctrm6720
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Interpreting GISTIC2 output
... I am wondering how to get GISTIC to output, or how to post-process, data that shows **copy number change per gene relative to a threshold for each sample**. According to [the GISTIC documentation][1], the "all_lesions" file should contain actual copy number information for each sample at each ampl ...
gistic written 3 months ago by vctrm6720
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HRD score LST?
... I am confused about the calculation of LST score for the HRD score. Looking at the description of such a package that does this calculation ([scarHRD](https://github.com/sztup/scarHRD)): In the LST figure B, I don't understand why the 2nd "X" in chromosome 1 is marked as an "X". It is between 2 ad ...
cnv written 3 months ago by vctrm6720 • updated 3 months ago by _r_am32k

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