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somatic

Here are 6 public repositories matching this topic...

sigven / pcgr

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Personal Cancer Genome Reporter (PCGR)

interpreter cancer clinical tumor vcf cancer-genomics reporting-engine copy-number-variation annotation-tool somatic cancer-variants annotation-framework snvs oncology-data precision-oncology variant-interpretation therapeutic-targets precision-cancer-medicine

Updated Jan 25, 2021
R

Sarek

SciLifeLab / Sarek

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Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

docker workflow bioinformatics pipeline genomics nextflow cancer somatic-variants reproducible-research containers next-generation-sequencing singularity badge reproducible-science travis-link somatic germline scilifelab gitter-badge germline-variants gitter-link scilifelab-link nextflow-link nbis-link ngi-link

Updated Jan 27, 2020
Nextflow

OpenGene / MutScan

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Detect and visualize target mutations by scanning FastQ files directly

visualization bioinformatics validation cancer detection ngs mutation variant fastq somatic

Updated Jan 21, 2020
C

nf-core / sarek

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Open

Add a key for VEP genome assembly

maxulysse commented Jan 26, 2021

It would be nice to add a params to choose the VEP genome assembly.
In most cases it is the --genome params, but I'm assuming it'll be easier to control if we have that as a separate params.
For example, it's currently not working with the --genome custom setting.

Read more

DSL2 enhancement good first issue

cancerit / dockstore-cgpwgs

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Dockstore implementation of CGP core WGS analysis

somatic-variants ngs snv indels dockstore somatic

Updated Jun 8, 2020
Shell

ammodramus / ebsom

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Empirical Bayes somatic variant calling

somatic-variants variant-calling somatic

Updated Oct 25, 2019
Python

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