extraction file for custom reference

[raval91]

Hello!

I have been trying to run HLA-LA but receive the following error

Have found no compatible reference specifications in /home/hisd/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at /home/hisd/HLA-LA/src/HLA-LA.pl line 364.

I have tried to create an extraction file based on the reference I used to align, and the output of idxstats... please see attached, the output of idxstats, and the extraction file I then created from it. Have I done something wrong when making the extraction file?

The extraction file was placed in both the graphs/PRG_MHC_GRCh38_withIMGT/knownReferences and src/additionalReferences/PRG_MHC_GRCh38_withIMGT/ directories.

GRCh38_latest_genomic.txt barcode01_idxstats.txt

Thank you for your help! Rohan.

[AlexanderDilthey]

Hi @raval91,

I think there are two issues:

• your idstats and the extraction file are not in sync - the extraction file should have 1 line for each line in idxstats, and this is not the case
• I think your extraction file misses some alternative MHC contigs, e.g. NT_187692.1, NT_167244.2 etc. - for these, you should set ExtractCompleteContigto 1. Compare with this file here, which also has alternative MHC contigs: https://github.com/DiltheyLab/HLA-LA/blob/master/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_3.txt

Best wishes

Alex