Reference Files for the given example VCF

[ALogandha]

Hi,

I am trying to run MuPeXi on the given example VCF (https://raw.githubusercontent.com/ambj/MuPeXI/master/data/example.vcf) using the below command but end up with error:

MuPeXI.py -v data/example.vcf -a HLA-A01:01,HLA-A02:02

I am using homo_sapiens_refseq_vep_104_GRCh38.tar.gz for VEP cache (http://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_vep_104_GRCh38.tar.gz) and fasta files downloaded from http://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens as the reference.

Please find the error message pasted below:

Reading in data
Creating proteome reference dictionary
Traceback (most recent call last):
File "MuPeXI/MuPeXI.py", line 1800, in
main(sys.argv[1:])
File "MuPeXI/MuPeXI.py", line 44, in main
proteome_reference, sequence_count = build_proteome_reference(paths.proteome_ref_file, input_.webserver, species)
File "MuPeXI/MuPeXI.py", line 280, in build_proteome_reference
proteome_reference[geneID][transID] += line.strip()
UnboundLocalError: local variable 'geneID' referenced before assignment

Could I request you to confirm I am using the correct references to run the example VCF?

I appreciate your help!

Thanks in advance.

Regards,
Ashmitaa.

[zyxNo1]

I have the same question. Any idea?