Pipeline Details
Name: GMS-Myeloid Pipeline
Version: v1.0
Contact Person: Ram
Location: /home/ramsainanduri/Pipelines/Validation_Documents/mkdocs_test
Description
This is Mk Docs pipeline. Test follows...
Minimum Requirements
Nextflow version: 19
List of Software Used
| ID | Tool/Software | Version | Build | Type | Availability | Container Name | External Contact Person If Any | Reference |
|---|---|---|---|---|---|---|---|---|
| 1 | BWA | v0.7.17-r1188 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/lh3/bwa/issues | open |
| 2 | CNVkit | v0.9.5 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/etal/cnvkit/issues | open |
| 3 | CNVkit | v0.9.9 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/etal/cnvkit/issues | open |
| 4 | delly | v0.8.7 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/dellytools/delly/issues | open |
| 5 | freebayes | v1.3.5 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/freebayes/freebayes/issues | open |
| 6 | GATK | v4.1.9.0 | HG19/HG38 | Open-Source | Container/Image | gatk_4.1.9.0.sif | https://github.com/broadinstitute/gatk/issues | open |
| 7 | Manta | v1.6.0 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/Illumina/manta/issues | open |
| 8 | MELT | v2.1.5 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | - | open |
| 9 | pindel | v0.2.5b9, 20160729 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/genome/pindel/issues (kaiye@xjtu.edu.cn) | open |
| 10 | R | v4.1.0 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://www.r-project.org/ | open |
| 11 | Sambamba | v0.8.0 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/biod/sambamba/issues | open |
| 12 | Samtools | v1.12 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/samtools/samtools/issues | open |
| 13 | Sentieon | v202010.01 | HG19/HG38 | Commercial | Container/Image | SomaticPanelPipeline_2021-06-24.sif | - | open |
| 14 | svdb | v2.2.0 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/J35P312/SVDB/issues | open |
| 15 | Vardict | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/AstraZeneca-NGS/VarDict/issues | open | |
| 16 | VCFtools | v0.1.16 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | https://github.com/vcftools/vcftools/issues | open |
| 17 | VEP | v95.3 | HG19/GRCh37 | Open-Source | Container/Image | container_VEP.sif | https://github.com/Ensembl/ensembl-vep/issues | open |
| 18 | VEP | v103.1 | HG38/GrCh38 | Open-Source | Container/Image | ensembl-vep_release_103.sif | https://github.com/Ensembl/ensembl-vep/issues | open |
| 19 | Vt | v0.5 | HG19/HG38 | Open-Source | Container/Image | SomaticPanelPipeline_2021-06-24.sif | Adiran (atks@umich.edu) | open |