gatk4-rnaseq-germline-snps-indels
Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
Requirements/expectations :
- uBAM
Output :
- A BAM file and its index.
- A VCF file and its index.
- A Filtered VCF file and its index.
Runtime parameters are optimized for Broad’s Google Cloud Platform implementation.
For program versions, see docker containers.
Important Notes :
- Runtime parameters are optimized for Broad’s Google
This is a companion discussion topic for the original entry at github.com/thouis/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels