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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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 ...
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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 ...
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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 ...
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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:
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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....
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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 ...
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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 ...
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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, ...
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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 ...
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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 ...
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