Specify reference to samtools index
I generated a cram using samtools:
samtools view -C -T <reference-file> -o sample.cram sample.bam
Now I want to index the cram and the reference file is not in the same location. I get errors like
Failed to populate reference for id 91
Failed to populate reference for id 92
I suspect they're because of the missing reference. But samtools index command does not take a reference. I tried -T, and --reference. Any ideas on getting around this problem?
Thank you
Manisha
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Is your cram file coordinate-sorted?
P.S.: Check about
$REF_PATHand$REF_CACHEon HTSLIB docs.The cram is coordinate-sorted. How can I check if it has M5 tags and what the value is? I am quite confused about what REF_PATH should be set to.