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adefelicibus / soap-hla

SOAP-HLA is a flow of sequencing data analysis pipeline to type all of the HLA genes in IMGT/HLA database using capture sequenced data or WGS data with high accuracy.
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soap-hla

SOAP-HLA is a flow of sequencing data analysis pipeline to type all of the HLA genes in IMGT/HLA database using capture sequenced data or WGS data with high accuracy.

Disclaimer: this is just a conda-package repository. You can read about the software in his paper:

An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing

Install

This package must be installed using conda:

conda install -c adefelicibus soap-hla

Using

Starting with a ready-to-use BAM file, you can run the software with this command:

source activate soap-hla
MHC_autopipeline -i sample.bam -od path/output/ -v hg19

Version 1.0.0