fcgportal

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...

Same here, neither samtools sort -n or sambamba sort -n works on my bam files. :(