I'm trying to follow the GATK Best Practices for Germline SNPs Indels workflow as independent steps in the command line locally or within a GATK Docker container (i.e. not on a cloud service). I don't see the individual steps that are implemented in the workflow.
Specifically, starting with data pre-processing for variant discovery, I first converted the fastq files to unmapped bam (gatk FastqToSam) and validated the output (gatk ValidateSamFile). Then, next steps are to Map to Reference using BWA & MergeBamAlignments. Going to bwa outside of the GATK container, it seems like I need to run bwa aln -b because I'm feeding it a bam file. After that MergeBamAlignments requires an OUTPUT (result of alignment?), REFERENCE_SEQUENCE (the original fasta file file that reads were aligned to, ie. hg38), and UNMAPPED_BAM (output of FastqToSam?). But when I feed those files to the MergeBamAlignments, I get an error.
So big picture, I'd like to see the steps that the workflow is implementing and, ideally, the individual commands that it's running to get there. Is something like this available?
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