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In the Step 5 - Single Nucleotide Variant calling cell by cell,
Could you tell me what the role of the SNPs descriptor file is?
Does it is the SNP calling results at the overall sample level, or is…
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I have a question regarding rank score penalty points which I assume is due to lack of "good enough" compound.
I found a missense variant and a SV (small deletion) in the gene FBP1 in our case 2433…
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Hi,
In the "All SNVs and INDELs" search option, would it be possible in future updates to add the field corresponding to the Inheritance model in the search results and as a search filter (genetic mo…
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It would be powerful to restrict the alignments shown in the alignment track to only those defined by the user in Region Navigator.
An example use case is if there are two SNVs in a tumour suppress…
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In one approach (fmt="vcf-simple"), use pandas instead of pysam to parse the VCF as a tabular file, but don't further parse the INFO and sample columns. This lets us read an arbitrary VCF, manipulate …
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While I'm not exactly sure what the standard says on whether fill or stroke attributes on the `use` element are taken into account or not, according to [this](https://developer.mozilla.org/en-US/docs/…
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Hi,
I am trying to use mmsig on the WGS data. My files are in hg38.
I am using COSMIC (v3.2) GRCh38 SBS as the reference file. I have also set refcheck = FALSE. Even then, few snvs are not reco…
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Our local geneticists are loo…
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Hi,
I am trying to call allelic CN values. I have a Mutect2 VCF, but I also have a curated list of germline SNVs that I got by filtering the Mutect2 VCF. I am wondering how to properly use either …
vymao updated
3 years ago
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For Ignacio:
_"
Dear Peter and Maxime,
I was just about to email you. We have updated the cloneHD SMC-Het Docker to be run with the settings we used for SMC-Het and for PCAWG. These changes are i…