Updating base image and converting germline rules - Githubissues

mtandon09 / CCBR_GATK4_Exome_Seq_Pipeline

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH

https://mtandon09.github.io/CCBR_GATK4_Exome_Seq_Pipeline/

MIT License

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Updating base image and converting germline rules #10

Closed skchronicles closed 3 years ago

skchronicles commented 3 years ago

Changelog

Removing bowtie exe path from fastq_screen config
Converting germline rules to use docker images
Adding tools WES Pipeline base image
- Control-FREEC
- Tabix
- Sambamba
- Sequenza
- Somalier
- VarScan
- GATK/3.8 (CombineVariants step not available in GATK4)