Hello,
I'm using Picard tools, for instance AddOrReplaceReadGroups, within a unix pipe like this one:
The output of the program is always in BAM format, if I use:
Is there a way to tell the program to write SAM format to STDOUT? This would be nice so I could further extend my pipeline.
I'm using Picard tools, for instance AddOrReplaceReadGroups, within a unix pipe like this one:
Code:
unpigz --stdout -p 1 mapped_reads.sam.gz | \ java -Xmx2g -jar AddOrReplaceReadGroups.jar INPUT=/dev/stdin OUTPUT=/dev/stdout \ RGLB=some RGPL=illumina RGPU=adapter RGSM=name > mapped_reads.bam
Code:
OUTPUT=/dev/stdout
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