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humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data
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missing chr6.fna #28

Closed cjieming closed 6 years ago

cjieming commented 6 years ago

Hi I am trying to use the script for preprocessing: get-reads-alt-unmap.sh

I realize however that the script looks for the fasta in the 'data/chr6/' folder, which contains the index files but do not have the corresponding fasta file. I am getting an error when i ran the script.

Help?

cjieming commented 6 years ago

Anyway I solved the issue after obtaining fasta for just chr6 from GRCh38 and then re-indexing using bwa, samtools and picard. I did it for one sample, and the accuracy seems good now. I will close this issue for now.