Can Picards AddOrReplaceReadGroups output SAM format to Pipe?

[kmpf]

Hello,

I'm using Picard tools, for instance AddOrReplaceReadGroups, within a unix pipe like this one:

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

The output of the program is always in BAM format, if I use:

OUTPUT=/dev/stdout

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.

[aggp11]

I don't know if this will work, but you could try to pipe the output to samtools view to try to get the SAM output. e.g.

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 | samtools view -h - > mapped.sam

The "-h" option would include the header in the output. I haven't tried this but I think this should work and this should be quick check.

Hope this helps!
Praful

[kmpf]

Thanks for your quick answer. I tried it the way you described it. It seems to work fine.

Eventhough this workaround works, it would have been nice of Picard to provide a defined switch to choose the output format.

Many thanks,
Christoph

[Timothy Amos]

Named pipe

Another solution is to make a named pipe i.e.:

mkfifo foo.sam

you should be able to set foo.sam as your output file, run that part of your pipeline in the background and use foo.sam as an input file in another command running at the same time. e.g.:

unpigz --stdout -p 1 mapped_reads.sam.gz | \
java -Xmx2g -jar AddOrReplaceReadGroups.jar INPUT=/dev/stdin OUTPUT=foo.sam \
RGLB=some RGPL=illumina RGPU=adapter RGSM=name &

java -Xmx1g program1.jar I=foo.sam O=/dev/stdout | java -Xmx1g program2.jar I=/dev/stdin O=/dev/stdout

See http://sourceforge.net/p/samtools/ma...sage/25870969/ for a discussion on piping and picard tools and the speed benefits of using uncompressed bam files over uncompressed sam files.

hth,

Tim