-
Great tool however, header is mangled. for example: main hg38 contigs (chr1-chrY) get chopped off in the output and only HLA contigs -> ALT contigs appended to the VCF header. please fix.
for examp…
-
###########error##########
getAllelesForAA(HLA_AA,"DQB1_77")
Error: allele DQB1*02:180 could not be found in the alignment file
Execution halted
#######################
I expected that midasH…
-
Hi,
I am trying to run "test_whole.sh" with example data "whole".
but it gives the following error at "phase_variants.py" step.
I lack novoalign lic so the script use bowtie2 instead.
Hoping …
-
When running "arcas genotype fastq1 fastq2" I consistently get the error that there is no such file or directory for hla_nom_p.txt. Specifically " No such file or directory: 'Desktop/anaconda3/share/a…
-
Two things to check for:
* There should not be more than 2 HLA code for HLA-A, HLA-B, HLA-C
* The input file for a list of pairs should be given to `multiprocess_aams.py` with the names of the…
-
### Installation Type
Docker
### pVACtools Version / Docker Image
griffithlab/pvactools:latest
### Python Version
_No response_
### Operating System
_No response_
### Describe the bug
I have …
-
Hello;
When I import .dmx of face modeldoc won't reconize like HLA model editor. HLA model editor reconize correcly and even I put compiled .vmdl_c to game reconize.
But when I import same .dmx wi…
-
### Installation Type
Docker
### pVACtools Version / Docker Image
latest
### Python Version
_No response_
### Operating System
Ubuntu
### Describe the bug
When running pvacseq to make predict…
-
Hey Michael,
For a current project we are working on, we are trying to use Sage with HLA peptides, specifically from the [thunderPASEF method](https://www.nature.com/articles/s41467-024-46380-y). W…
-
I have been trying to run ```g2gtools patch``` and ```g2gtools transform``` but encounter errors like:
`[g2gtools] Error: invalid literal for int() with base 10: '02N'`
`[g2gtools] Error: invalid …