Can I create a CRAM file with a relative reference path? I’m trying to create a CRAM file that stores its path to the FASTA reference as a relative path, rather than an absolute path, so that I can move the files around. Unfortunately I can’t get this to work; I was expecting the following to work:

⟩⟩⟩ samtools view -C -T ../reference/ref.fa -o output.cram input.bam


However, the resulting file contains an absolute path in its header:

⟩⟩⟩ samtools view -H output.cram
…
@SQ     SN:1    LN:249250621    M5:hash     UR:/absolute/path/to/data/mapped/../reference/ref.fa
…


As a result, I am unable to open the file via a different path mount that results in different absolute paths, and I can’t move the file (+ its reference) around, or to different machines.

I know that I could set the REF_PATH environment variable or specify -T when reading the file but I would like to avoid this (the result file needs to be readable by IGV, launched by users who don’t know how to set environment variables).

Is there a way of creating a CRAM file that stores a relative path to its reference?
In your CRAM file, make all of the reference sequences present in the ./ directory. Then make a bash script to make relative links to your reference for whatever mount you are using at the time - ie ln -s TARGET LINK_NAME. 

Now your CRAM is portable and you just have to tailor the local working dir to it.