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?