Hi there,
I've run into a problem and I can't solve it with Google-fu
I got my CRAM from Nebula Genomics and was wanting to use WGSExtract on it but WGSExtract says that it isn't indexed or sorted but when I try to view or sort it in samtools it tells me:
Failed to populate reference for id 0
Unable to fetch reference #0 10000..39404
Failure to decode slice
[main_samview] truncated file.
I really don't know if it's something to do with my install of samtools not working or if I need to do something else to the Nebula Genomics CRAM file.
I tried it also on my brother's file from Nebula and samtools says the same thing to me so I don't think the file can be 'bad'
If it makes a difference I'm using Ubuntu WSL
Does anybody out there know what I can do about this problem? Thanks.
Are you providing correct reference file?
Thanks GenoMax I'm not providing any out of sheer ignorance.
I wouldn't even know what the correct reference fie would be, where I might get it, or how I might make samtools aware of it.
You will need to find out from Nebula which reference file they used to create the CRAM. Manipulations with CRAM file will need the reference. See: https://www.htslib.org/workflow/cram.html
Thanks GenoMax, much obliged, I shall see what they have to say about it.