pipeline-call-sSNV Flow Diagrams and Tool Links

Variant Calling

SomaticSniper

Diagram

Tools

SomaticSniper

SomaticSniper source: https://github.com/genome/somatic-sniper Version: SomaticSniper v1.0.5.0 (Released on Jul 16, 2015) GitHub Package: ghcr.io/uclahs-cds/somaticsniper:1.0.5.0

bam-readcount

bam-readcount source: https://github.com/genome/bam-readcount Version: v0.8.0 Release (Released on Oct 21, 2016) GitHub Package: ghcr.io/uclahs-cds/bam-readcount:0.8.0

Strelka2

Diagram

Tools

Manta

Manta source: https://github.com/Illumina/manta Version: v1.6.0 (Released on Jul 9, 2019) GitHub Package: ghcr.io/uclahs-cds/manta:1.6.0

Strelka2

Strelka2 source: https://github.com/Illumina/strelka Version: v2.9.10 (Released on Nov 7, 2018) GitHub Package: ghcr.io/uclahs-cds/strelka2:2.9.10

Mutect2

alt text

Tools

GATK

GATK source: https://github.com/broadinstitute/gatk Version: 4.2.4.1 (Released on Jan 4, 2022) Docker Image: broadinstitute/gatk:4.2.4.1

MuSE

alt text

Tools

MuSE

MuSE source: https://github.com/wwylab/MuSE Version: 2.0 (Released on Aug 25, 2021) GitHub Package: https://github.com/uclahs-cds/docker-MuSE/pkgs/container/muse

Variant Intersection

alt text

Tools

BCFtools

BCFtools source: https://samtools.github.io/bcftools Version: 1.17 (Released on Feb 21, 2023) GitHub Package: https://github.com/uclahs-cds/bcftools:1.17

VennDiagram

VennDiagram source: https://github.com/uclahs-cds/public-R-VennDiagram Version: 1.7.3 (Released on Apr 12, 2022)

vcf2maf

vcf2maf source: ghcr.io/mskcc/vcf2maf/vcf2maf Version: v1.6.18 GitHub Package: https://github.com/mskcc/vcf2maf