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ssadedin / bazam

A read extraction and realignment tool for next generation sequencing data
GNU Lesser General Public License v2.1
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Compressed output #14

Open BrianLohman opened 5 years ago

BrianLohman commented 5 years ago

Hi,

I am using bazam to convert CRAM to FASTQ and it is working well. However, it would be very helpful if the output was gzip compressed. Would you consider adding this? It would greatly reduced disk space needed while working on AWS.

Thanks

fcgportal commented 2 years ago

You can pileup the interleaved fastq from Bazam into reformat.sh and output separated paired fastq.gz files. It works fine for me.

java -jar build/libs/bazam.jar -bam test.bam | reformat.sh int=t in=stdin.fq out1=out_r1.fastq.gz out2=out_r2.fastq.gz