Save alignments directly in BAM in arcad-hts_4_mapping

SouthGreenPlatform / arcad-hts

Scripts for the analysis of high-throughput sequencing data from the ARCAD project.

http://www.arcad-project.org/

GNU General Public License v3.0

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Save alignments directly in BAM in arcad-hts_4_mapping #17

Open timflutre opened 9 years ago

timflutre commented 9 years ago

Instead of doing "bwa ... > out.sam" and then "samtools view -b out.sam > out.bam", we could use a pipe. This will save disk space, and may even be faster (less I/O needed).