How to convert CRAM back to BAM using samtools

[hthl85]

Hello everyone,

I just installed samtools v1.0 and want to test CRAM feature. I converted .BAM file to .CRAM and It was successful. Now I want to convert back .CRAM to .BAM but don't know how to do that. Does anyone know how to do that? Please show me. Thank you.

[dpryan]

It's the same command, just use the -b option instead of -C.

[hthl85]

It's the same command, just use the -b option instead of -C.

Thank you for your quick response. I will try and let you know the result.

[hthl85]

It's the same command, just use the -b option instead of -C.

Hello Devon Ryan,
Can you please help me check my command is correct or not?
samtools view -T <fasta_path> -b -o <bam_file_path> <cram_file_path>.

I ran this command and got the error 'Servname not supported for ai_socktype'

Thank you for your time.

[dpryan]

Are you running this on amazon e3 or something like that? This error message will normally only happen if there's some issue regarding networking (generally receiving an IP when a name is expected or vice versa).

[hthl85]

Are you running this on amazon e3 or something like that? This error message will normally only happen if there's some issue regarding networking (generally receiving an IP when a name is expected or vice versa).

I will contact with my admin to fix this problem. Thank you very much.