Commit 5d4fca8a authored by van den Berg's avatar van den Berg
Browse files

Do not write MarkDuplicates PG tag for every read

This is supposed to speed up MarkDuplicates by up to 16%, see
https://github.com/broadinstitute/picard/issues/902 for details.
parent c4ea41c5
Pipeline #4112 passed with stages
in 24 minutes and 48 seconds
......@@ -138,6 +138,7 @@ rule markdup:
containers["picard"]
shell:
"picard -Xmx4G -Djava.io.tmpdir={input.tmp} MarkDuplicates "
"PROGRAM_RECORD_ID=null "
"CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
"{params.bams} OUTPUT={output.bam} "
"METRICS_FILE={output.metrics} "
......
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