tmhmxg59

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xHLA invalid input file, /get-reads-alt-unmap.sh not working.

Did you read [35](https://github.com/humanlongevity/HLA/issues/35)? I think it might help.

[E::bwa_idx_load_from_disk] fail to locate the index files when running

I believe you are missing fna, as @cjieming noted. https://github.com/humanlongevity/HLA/issues/27 https://github.com/humanlongevity/HLA/issues/35

get-reads-alt-unmap.sh get "[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!"

I think [bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort! is your main issue. I think this is because you are missing .fna and/or proper bwa index.

get-reads-alt-unmap.sh get "[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!"

I get those warnings too. I'm not sure if they are significant or not. I tried resorting and removing unpaired reads (not sure if I was successful), but the warnings...

Cut ties to specific build?

Please forgive my naïveté, but could someone suggest steps to use a GRCh37 aligned BAM? Like is it best to start with fq and realign or is there an easier...

Cut ties to specific build?

In my hands, the provided get-reads script worked well for conversion from GRCh37 to GRCh38. https://github.com/humanlongevity/HLA/issues/35

how to use get-reads-alt-unmap via docker?

And/or check out https://github.com/humanlongevity/HLA/issues/35