No compatible reference

DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data

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No compatible reference #24

Closed sethsh7 closed 4 years ago

sethsh7 commented 4 years ago

Hello

I'm having issues with "no compatible reference" as I think the reference my CRAM files are aligned to is slightly non standard. I wonder if you could generate an additional known reference file from my samtools index?

Many thanks Seth idxstats.txt

AlexanderDilthey commented 4 years ago

Hi Seth,

Yes, that's right. Yes, we can generate such a file for you! Does your reference genome include any MHC alternative contigs?

Best,

Alex