• Introduction
• Scripts
  • hisatgenotype.py – Analysis of a whole human genome
  • hisatgenotype_locus.py – Analysis of a specific gene, genomic region, or gene family
    • For advanced users
  • hisatgenotype_build_genome.py – Building a genotype genome
  • hisatgenotype_extract_vars.py – Extraction of variants, haplotypes, etc.
  • hisatgenotype_extract_reads.py – Extraction of reads that belong to genomic regions of interest
  • hisatgenotype_locus_samples.py – Analysis of many samples

Introduction

This is the old manual for versions earlier than 1.1. Please use this information for those versions only.

Scripts

hisatgenotype.py – Analysis of a whole human genome

The hisatgenotype.py python script will analyze a whole human genome using whole genome sequencing reads. It will align reads to genotype genome, extract reads belonging to each locus of interest, and perform typing and assembly.

Examples:

$ hisatgenotype.py --base genotype_genome -p 4 -1 read.1.fq.gz -2 read.2.fq.gz
$ hisatgenotype.py --verbose --base genotype_genome -p 4 --region-list hla.A -1 read.1.fq.gz -2 read.2.fq.gz
$ hisatgenotype.py --base genotype_genome --alignment-file NA12878.bam  
$ hisatgenotype.py --base genotype_genome --region-list hla.A,hla.B,hla.C,hla.DQA1,hla.DQB1,hla.DRB1,codis,cyp.2D6 --alignment-file NA12878.bam

hisatgenotype_locus.py – Analysis of a specific gene, genomic region, or gene family

The hisatgenotype_locus.py python script will analyze a particular locus or a set of genes or genomic regions using extracted reads. As the name of the script (locus) implies, it will align reads to a part of genotype genome and perform typing and assembly.

Examples:

 $ hisatgenotype_locus.py --base hla --locus-list A --num-editdist 2 --assembly -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz
 $ hisatgenotype_locus.py --base hla --locus-list A,B,C,DQA1,DQB1,DRB1 --num-editdist 2 -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz

For advanced users

In addition to analyzing real sequencing reads, the script comes with additional testing capabilities, which might come in handy when determining whether a problematic result is due to noise in sequencing reads or algorithms. To do so, the script can generate simulation reads with sequencing errors and SNPs, and test and evaluate the accuracy of its typing and assembly algorithms, with additional options described below.

Examples:

 $ hisatgenotype_locus.py --base hla --locus-list A 
 $ hisatgenotype_locus.py --base hla --locus-list A --debug "pair"
 $ hisatgenotype_locus.py --base hla --locus-list B --assembly --debug "pair,test_list:A*03:01:01:05,A*24:02:01:01"
 $ hisatgenotype_locus.py --base hla --locus-list A --assembly --simulate-interval 10 --perbase-errorrate 0.3 --perbase-snprate 0.1 --num-editdist 2 --debug "pair,full"
 $ hisatgenotype_locus.py --base hla --locus-list A --assembly --simulate-interval 10 --perbase-errorrate 0.3 --perbase-snprate 0.1 --num-editdist 2 --debug "pair,full" --skip-fragment-regions 1000-1020 --random-seed 0

hisatgenotype_build_genome.py – Building a genotype genome

The hisatgenotype_build_genome.py python script will create a genotype genome using the human reference genome (GRCh38) and several genomic databases. A tutorial for the script can be found here.

Examples:

 $ hisatgenotype_build_genome.py -p 4 --base genotype_genome --database-list hla --commonvar
 $ hisatgenotype_build_genome.py -p 4 --base genotype_genome --database-list hla,codis,cyp --commonvar

hisatgenotype_extract_vars.py – Extraction of variants, haplotypes, etc.

This hisatgenotype_extract_vars.py python script is typically run by other scripts, though instructions are provided here for users who wish to directly run the script. The script will extract allele sequences, variants, haplotypes, etc. from multiple sequence alignments available in hisatgenotype_db. Tutorials for the script can be found at HLA typing and DNA fingerprinting anlaysis.

Examples:

 $ hisatgenotype_extract_vars.py --base hla --locus-list A,B,C,DQA1,DQB1,DRB1 --min-var-freq 0.1
 $ hisatgenotype_extract_vars.py --base codis

hisatgenotype_extract_reads.py – Extraction of reads that belong to genomic regions of interest

The hisatgenotype_extract_reads.py python script will extract reads that belong to loci of interest from whole sequencing reads. The script can also be used to extract reads from many samples. A tutorial for the script can be found here.

Examples:

 $ hisatgenotype_extract_reads.py --base genotype_genome --database-list hla,codis,cyp -1 test.1.fq.gz -2 test.2.fq.gz
 $ hisatgenotype_extract_reads.py --base genotype_genome --database-list hla,codis,cyp --read-dir test_input --out-dir test_output

hisatgenotype_locus_samples.py – Analysis of many samples

The hisatgenotype_locus_samples.py python script will analyze genomic regions of interest using reads that are extracted from using hisatgenotype_extract_reads.py. Please avoid directly running the script on whole genomic sequencing reads as doing so will lead to inaccurate results due to reasons partly described here. A tutorial for the script can be found at HLA typing. The script is designed to analyze many samples.

Examples:

 $ hisatgenotype_locus_samples.py -p 4 --region-list hla --read-dir test_input --out-dir test_output
 $ hisatgenotype_locus_samples.py -p 4 --region-list hla.A,hla.B --read-dir test_input --out-dir test_output
 $ hisatgenotype_locus_samples.py -p 4 --region-list codis --read-dir test_input --out-dir test_output