Closed IanSudbery closed 5 years ago
pipeline_bamstats uses bam2bam in order add back peduoquality/seqeuence to a bam file.
pipeline_bamstats
bam2bam
if does with the following command:
cat Aly-IN-2.bam | cgat bam2bam -v 0 --method=set-sequence > BamFiles.dir/Aly-IN-2.bam
I.e. output is sent to stdout, but the log is not redirected. bam2bam doesn't like this, even though -v0 is set, which should probably be okay (see cgat-developers/cgat-apps#30), but it isn't currently..
-v0
Acribbs
commented
5 years ago
pipeline_bamstatsusesbam2bamin order add back peduoquality/seqeuence to a bam file.if does with the following command:
I.e. output is sent to stdout, but the log is not redirected.
bam2bamdoesn't like this, even though-v0is set, which should probably be okay (see cgat-developers/cgat-apps#30), but it isn't currently..