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GitHub / jfnavarro / hla_pipeline
DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions
JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jfnavarro%2Fhla_pipeline
Stars: 8
Forks: 2
Open Issues: 11
License: mit
Language: Python
Repo Size: 1.55 MB
Dependencies:
32
Created: about 4 years ago
Updated: 9 months ago
Last pushed: almost 3 years ago
Last synced: 8 months ago
Topics: dna, hla, mhc, neoantigens, rna, wes, wgs
Files
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Readme
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Dependencies
environment.yml
conda
- bcftools
- bedtools
- biopython
- bwa
- ensembl-vep 102.0.*
- gatk4-spark
- kallisto
- mhcflurry
- optitype
- picard
- python 3.6.1.*
- qualimap
- samtools
- somatic-sniper
- star
- subread
- tensorflow 1.15.0.*
- trim-galore
- varscan
- vcfpy
- vcftools
- yara