Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
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added support for --variant_ready_bam to skip over all the bam proces… #89
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brianjohnhaas closed 3 years ago
allow for using --variant_ready_bam bams (so no need for splitNcigar, etc.) and just call variants.
also, included "haplotype_caller_xtra_args" parameter so we can add custom parameters to the haplotypecaller step.