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5.2 years ago
Hadi M
▴
50
Hi, I am working with limited amount of disk space so I want to know if it possible to pipe BWA MEM to Picard SortSam? If so, what would be the proper command for it? I want to skip the SAM file and directly sort and convert it to BAM.
I do aware I can pipe BWA MEM to Samtools Sort but I plan to stick with GATK best practices as much as possible.