PMalleleFinder

Table of contents

• General info
• Requirements
• Setup
• Command line options

General info

This pipeline will allow you to extract allele sequences and population information for TR genes.

Requirements

• python=3.7.1
• biopython=1.76
• BCBio.gff=0.6.6
• pandas=1.0.1
• numpy=1.18.1
• R=3.6.1
• samtools=1.6
• tabix=1.6
• dplyr=0.8.5
• tidyr

Setup

Clone the project structure and run main_pipe.py

Example usage:

$ python3 main_pipe.py --gff=gencode.v32.chr_patch_hapl_scaff.annotation.gff3 --vcf="ALL.chr7.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz;ALL.chr14.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz" --popfile=pop-info.tsv --ref=GRCh38_full_analysis_set_plus_decoy_hla.fa

Command line options

• --gff=gencodefile required This option required a .gff or .gff3 input file to read gene locations from
• --vcf=vcffile.vcf required This option requires a .vcf.gz file. A .vcf.tbi file is also required to be present in the same location to extract variation.
• --popfile=populationfile required This option requires a tab seperated population file in the format of sample pop super_pop
• --ref=reference.fasta required This option requires the reference genome fasta. It is also required to have a index fasta file in the form of a .fai file present in the same folder.
• --filter=filterfile This option allows the specification of genes to filter on. Every new filter should be on a new line in this file. If there is no filter specified the pipeline will assume TCR genes. Chromosones can be filtered by adding #CHR int,int on the first line of the filter file.
• --threshold=integer This option allows the specification of the threshold used to discard sequences. If not specified the threshold is set to 4.
• --rss=TRUE|FALSE This option if set to TRUE will also generate sequences containing the RSS for V,D,J genes. 60bp sequence will be cut.
• --outdir=dir This option will change the output directory to a desired string. ex: output/test. When no output directory is specified the time of task start will be used as directory.