Hi all, I received some cram files from the 1000 genomes data. I am trying to convert them back to a fastq file, but can't seem to figure out how to do this. I've tried using
samtools fastq -1 out.R1.fastq -2 out.R2.fastq input.cram
but when doing this, I get an error of:
Failed to populate reference for id 0 Unable to fetch reference #0 9999..134549 Failure to decode slice [M::bam2fq_mainloop] processed 0 reads
I guess I can convert these back to a bam file, then convert them to a fastq, but this seems like a lot of unnecessary steps. I would think that there would be a straight forward approach to go directly from a cram to fastq, but can't seem to find a good solution.
Thanks for any help.