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Questions tagged [somatic]

Referring to the soma, i.e. non-germline cells in the body. The somatic genome is not inherited. Somatic mutations can lead to cancer. Somatic variant calling differs from germline variant calling because one often expects a mixture of mutated cells and non-mutated cells.

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How to adjust cutoffs in Mutect2

I'm currently performing some initial analyses on targeted Illumina sequencing data generated with DNA from diseased tissue. My hypothesis is that one particular gene might contain somatic mutations ...
Nereus's user avatar
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ERROR IN FUNCOTATOR: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)

I ran the "funcotator" step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of filtermutectcalls as input, but ...
Rita Soares's user avatar
3 votes
2 answers
299 views

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

I don't know if I'm in the right place but I have a technical problem to fix. I would have to align paired-end reads from Illumina sequencing to compare a normal genome with a tumor one. When I align ...
cucalorda's user avatar
2 votes
1 answer
257 views

somatic SNV tool for ONT samples

I'm looking for a tool to call somatic single nucleotide variations on reads from an Oxford Nanopore Technologies (ONT) run. I have both tumor and normal samples and have already aligned them to a ...
Walter Gallego Gómez's user avatar
2 votes
0 answers
599 views

What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?

This question was also asked on Biostars Consider this minimal VCF file which contains a multi-allelic call made by a somatic variant caller on a human tumor sample: ...
terdon's user avatar
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1 answer
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polidy VCF file for Canvas somatic-wgs cnv calling

I am trying to run Illumina CANVAS cnv caller for Somatic-WGS. There is an option "--ploidy-vcf" which is mandatory to supply, but don't know what exactly that mean. I had supplied the CNV....
Praveen's user avatar
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1 vote
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Somatic mutations for normal WES samples

I am trying to identify somatic mutations on healthy subjects (specifically in WES samples). As of now, I have found a couple of papers who have done similar studies such as this paper where somatic ...
Lot_to_learn's user avatar
0 votes
1 answer
529 views

What samples can be used for a Mutect2 Panel of Normals

I'm working on calling somatic variants from solid tissue tumors. I have one normal and one tumor sample for each patient. I plan to use Mutect2 to call somatic variants after preprocessing the data ...
Tomas Bencomo's user avatar
2 votes
1 answer
248 views

How to get unique somatic mutations for each individual patients

I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, ...
Lot_to_learn's user avatar
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1 answer
106 views

Information about control data

I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation ...
Lot_to_learn's user avatar
1 vote
1 answer
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Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?

I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions. I was looking for GATK best practices (like ...
gc5's user avatar
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