converting cram to ubam

Question

[joe_genome]

How can I convert a cram to an unmapped bam file with samtools?

samtools view -b -T ref.fasta input.cram > output.bam

is this correct?

[Ram]

I'm curious - why do you want to do this? Are you submitting reads from your on premises CRAM archive to something like GEO or SRA?

[joe_genome]

Correct this is what I'm doing

Answer 1

[Pierre Lindenbaum]

samtools collate -O -u input.cram | \
  samtools reset -O BAM -o out.bam