I would like to run 150 WGS samples through the GATK Best Practices workflow on Google Cloud Platform and have found that many of the workflows are optimized for hg38. Is there a way to use b37 instead with these workflows?
Given there are various workflows available, I'd also like to know which is recommended if I'd like to go from FASTQ files to a multi-sample VCF output from Joint Genotyping. I understand that I'd first need to use seq-format-conversion to go from paired FASTQ to uBAM. I'm not sure which of the following workflows would be best to get me from uBAM to multi-sample VCF: gatk4-data-processing, gatk4-germline-snps-indels, broad-prod-wgs-germline-snps-indels, gatk4-genome-processing-pipeline.
I'd appreciate your thoughts on this.
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