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openvax / vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy
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ValueError: Unable to infer reference genome #192

Open Shuhui-d opened 3 years ago

Shuhui-d commented 3 years ago

When I run the code as below

vaxrank \ --vcf /mydata.vcf \ --bam /mydata.bam \ --vaccine-peptide-length 25 \ --mhc-predictor netmhc \ --mhc-alleles H2-Kb,H2-Db \ --padding-around-mutation 5 \ --output-ascii-report vaccine-peptides.txt \ --output-pdf-report vaccine-peptides.pdf I got the Error saying: ValueError: Unable to infer reference genome for /mydata.vcf

mydata was the somatic variants called from hg19, do I run pyensembl install --release 75 --species human before this. I used the physical computer with Win10 system and installed VMwareWorkstation (Centos8). Should the vaxrank work like the codes above? Did I do any thing wrong? Looking forward to your reply. Thank you for helping!

leldershaw commented 3 years ago

I had this issue too, but I looked at vaxrank --help which suggests adding --genome hg19 to your command.

--genome GENOME
What reference assembly your variant coordinates are using. Examples: 'hg19', 'GRCh38', or 'mm9'. This argument is ignored for MAF files, since each row includes the reference. For VCF files, this is used if specified, and otherwise is guessed from the header. For variants specfied on the commandline with --variant, this option is required.