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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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error after only use chr6 mapping #88

Closed ksmpooh closed 1 year ago

ksmpooh commented 1 year ago

Hello

I tried to use HLA region targeted sequencing and only chr6 mapped bam file (both hg19 and GRch38), and running HLA*LA

error massage like this : Have found no compatible reference specifications in /usr/local/bin/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at /usr/local/bin/HLA-LA/src/HLA-LA.pl line 309.

Before this, it was mapped by whole reference genome (hg19), it worked well. But I just extracted chr6 from reference fasta, and mapped , it did not work.

Anyone knows these problems, please help me~

Thanks~

AlexanderDilthey commented 1 year ago

Hi @ksmpooh,

It seems that this is basically the same issue as here: https://github.com/DiltheyLab/HLA-LA/issues/89 - and the solution would be identical, i.e. you can create a reference specification file for your reduced reference genome, and everything should work fine. Let me know if you require assistance.

Best wishes

Alex