KIR_project

This is a repository to reproduce our KIR genotyping method (Sakaue et al.)

Overview

What variation exists in KIR region?

There are three levels of variations in KIR genes, and we address determining these variations using target sequencing data and our bioinformatics pipeline.

Standardized mapping pipeline using NGS-based target sequencing

01_Map_to_KIRreference.sh is our mapping script using picard and bwa mem.

Var	Descriptions
SAMPLEPATH	Path to the fastq files
ID	Sample ID to be used in bam files
BAMPATH	Path to the output bam files
COVERAGE	Path to the depth of coverage (to be used to determine the copy number)

KIR copy number estimation

02_determine_copy_number.py is a script to determine the copy number of each KIR genes using KIR3DL3 as a reference, using Kernel Density Estimation.

Var	Descriptions
input_csv	A csv file describing each KIR gene (row)'s mean depth per sample (column)
output_ploidy_file	Output file indicating an estimated ploidy per sample per gene (per each line)

HaplotypeCaller and JointGenotype

Using the bam file and KIR copy number obtained in the previous steps, we can call genotypes per sample per gene by using HaplotypeCaller with 03_HC.by_ploidy.sh, and jointly genoype across samples by 04_JG.by_ploidy.sh.

Var	Descriptions
GENE	A gene to call genotype
PLOIDY	Number indicating the ploidy (copy number) per gene per sample (integer)
GVCFPATH	Path to output GVCFs

DeepVariant

We use specific indels to determine KIR alleles. For that purpose, 05_run_deepvariant.sh can do genotyping using DeepVariant.

Var	Descriptions
DeepVariantPATH	Path to output DeepVariant VCFs and GVCFs

KIR allele determination

06_genotype_call_with_ploidy.py can determine possible KIR allele combination(s) per gene per sample.

Var	Descriptions
per_sample_vcf_file	output GVCFs/DeepVariant GVCFs (Note to split the multiallelic variants)
output_allele_file	output file for possible KIR allele combination(s)
dosage_file	interim file for collecting variant information
reference_file	interim file for collecting reference variant information

Contact

Questions to: ssakaue_at_broadinstitute.org