4 votes
Accepted

How to adjust cutoffs in Mutect2

Mutect2 uses a statistical model based on the available reads. Unlike with some other tools, there is not threshold based on depth or VAF or QUAL. The main statistic that does govern emission is the ...
Yossi Farjoun's user avatar
4 votes
Accepted

How to get unique somatic mutations for each individual patients

If what you want is to split the main VCF file into 1 file per sample, you could use bcftools query and view commands. A similar question was asked on biostars, adapting Jorge Amigo's solution to ...
cmdoret's user avatar
  • 595
3 votes
Accepted

What can be the bias of aligning paired-reads in a single-end mode?

In principle one should simply not align paired-end reads as if they were single end reads, not only because you are not taking advantage of the forward/reverse information contained in the reads, but ...
JRodrigoF's user avatar
  • 827
2 votes

Information about control data

Without control data from your subjects, I don't think there's really no way to distinguish somatic mutations from germ-line mutations. The best you can do is to screen out common variants, which are ...
heathobrien's user avatar
  • 1,816
2 votes
Accepted

What samples can be used for a Mutect2 Panel of Normals

As suggested by @burger in their comment, you can indeed use solid tissue samples as normals for your PON. You are clearly aware, but I want to spell this out for others, that there are a few caveats ...
Geraldine_VdAuwera's user avatar
1 vote

What can be the bias of aligning paired-reads in a single-end mode?

I tried to give me this explanation: with single-end alignment of paired-end reads, losing the directionality of the reads and also the expected fragment length, the R2 no longer maps if it maps the ...
cucalorda's user avatar
1 vote
Accepted

somatic SNV tool for ONT samples

ClairS is now released for long-read somatic variant calling. https://github.com/HKU-BAL/Clairs
Laurent's user avatar
  • 26
1 vote

polidy VCF file for Canvas somatic-wgs cnv calling

It seems you need to supply vcf files specifying the ploidy of the sex chromosomes. See https://github.com/Illumina/canvas/issues/89 for explanation and example vcf files.
Florian's user avatar
  • 11
1 vote
Accepted

Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?

Those will have to be treated as separate analysis. You can use Mutect or VarScan for the matched samples and the tools listed in the other question for the unmatched samples however that means that ...
Bioathlete's user avatar
  • 2,574

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