fastq for paired-end sequencing

[vcaropr1]

I am trying to create fastq file(s) for each respective read group within the cram file. There should be a total of 4 different files instead of the 1 large fastq file that has been made. Are there any special parameters that need to be added if this is possible through cramtools?

java -jar cramtools-3.0.jar \ fastq \ -I cram_file.cram \ -R ref_genome \

[vadimzalunin]

in the current implementation cramtools does not split data by read group. I've opened an issue: https://github.com/enasequence/cramtools/issues/50

[vcaropr1]

Thanks!