liftover

     

This script performs the conversion of genomic coordinates from Human Genome version 19 (hg19) to version 38 (hg38) using the liftover plugin from bcftools.

It takes a tab-separated values (TSV) file as input. This file should contain variant information with columns denoting chromosome (chr), position (pos), identifier (id), reference allele (ref), and alternate allele (alt).

Tip

Advantage of using BCFtools/liftover over other tools: Comparison of features and limitations across BCFtools/liftover, Transanno/liftover, Genozip/DVCF, GenomeWrap, Picard/LiftoverVcf and CrossMap/VCF

Genovese, Giulio, et al. "BCFtools/Liftover: An Accurate and Comprehensive Tool to Convert Genetic Variants across Genome Assemblies." Bioinformatics, vol. 40, no. 2, 2024, https://doi.org/10.1093/bioinformatics/btae038.

Quickstart

cd liftover
make help

INSTALLATION
        Usage: make install SRC=/path/to/your/directory
        SRC is optional. If SRC is not provided, the files are downloaded to the current directory.

LIFTOVER
        Usage: make liftover VAR_TAB_FILE=test/test.tsv OUT_PREFIX=test_prefix OUT_DIR=test/ SRC=/path/to/your/directory
        OUT_DIR is optional. If OUT_DIR is not provided, the output will be stored in the current directory.
        SRC is optional. If you used a different directory for installation, then specify the path SRC=/path/to/your/directory

Installation

Important

Please note that this script requires python3 and the pandas library. However, if you are using the Docker image, these requirements are already included in the image.

To install the necessary tools, which include bcftools, htslib, and the liftover plugin, and to download the required genome files (hg19.fa, hg38.fa and hg19ToHg38.over.chain.gz), execute the following command:

cd liftover
make install

This command will also create a directory named genomes and store the downloaded genome files in it. If SRC is not provided, the files are downloaded to the current directory.

Liftover

Using the Makefile (recommended)

cd liftover
make liftover VAR_TAB_FILE=/path/to/your/input_tab_file.tsv OUT_PREFIX=output_prefix

Parameters

• VAR_TAB_FILE: The input file should be a tab-delimited file containing the following columns: chr, pos, id, ref, and alt.
• OUT_PREFIX: Prefix for the output file.
• OUT_DIR: Output directory. (optional)
• SRC: Path to the directory if make install SRC=/path/to/your/directory was used during installation. (optional)

Using the Bash script

After installing the necessary tools and downloading the required genome files using the steps provided in the "Installation" section, you can run the script as follows:

cd liftover
bash liftover_hg19_to_hg38.sh <input_tab_file> <output_prefix> <output_directory>

Parameters

• input_tab_file: The input file should be a tab-delimited file containing the following columns: chr, pos, id, ref, and alt.
• output_prefix: Prefix for the output file.

Using Docker

This package is also available as a Docker image, which can be pulled from the GitHub Container Registry using the following command:

docker pull ghcr.io/maurya-anand/liftover

You can run the Docker image as follows:

cd liftover
docker run -v $(pwd):/data -it ghcr.io/maurya-anand/liftover /scripts/liftover_hg19_to_hg38.sh /data/test/test.tsv docker_test /data

The output from the above command will be saved in a directory named docker_test_liftover_results in your current directory.

In this command, -v $(pwd):/data mounts your current directory to the /data directory in the Docker container.

Replace /data/test/test.tsv with your input file, docker_test with your desired output prefix, and /data with your desired output directory.

Example usage

Warning

The script assumes that the liftover plugin and reference genomes are located in specific directories generated via make install command. These paths may need to be adjusted based on your specific setup. The script also assumes that the input file is properly formatted and contains the necessary columns.

Input file

cat test/test.tsv

1	818046	.	T	C
2	265023	.	C	A
3	361463	3:361463:G:T	G	T

Execution

cd liftover
make liftover VAR_TAB_FILE=test/test.tsv OUT_PREFIX=test_set

This command will create a directory named <prefix>_liftover_results, where <prefix> is the provided prefix, and save the output in a TSV file named <prefix>_lo_variants.tsv.

Each variant is represented as a row with the following columns:

• chr: The chromosome where the variant is located in the target genome assembly.
• pos: The position of the variant on the chromosome in the target genome assembly.
• ref: The reference allele in the target genome assembly.
• alt: The alternate allele in the target genome assembly.
• source: Additional information about the variant in the original genome assembly. This includes:
  • SRC_CHROM: The chromosome where the variant is located in the original genome assembly.
  • SRC_POS: The position of the variant on the chromosome in the original genome assembly.
  • SRC_ID: The identifier of the variant in the original genome assembly.
  • SRC_REF_ALT: The reference and alternate alleles in the original genome assembly.

Output file

cat test_set_liftover_results/test_set_lo_variants.tsv

chr1	882666	T	C	SRC_CHROM=1;SRC_POS=818046;SRC_ID=.;SRC_REF_ALT=T,C
chr2	265023	C	A	SRC_CHROM=2;SRC_POS=265023;SRC_ID=.;SRC_REF_ALT=C,A
chr3	319780	G	T	SRC_CHROM=3;SRC_POS=361463;SRC_ID=3:361463:G:T;SRC_REF_ALT=G,T

Steps

1. Convert the tab-delimited file to a VCF file using the convert_tsv_to_vcf.py Python script.
2. Compress the VCF file and generate the index.
3. Perform a liftover operation to convert the variants from one genome build to another using bcftools liftover plugin.
4. Normalize the VCF file using bcftools.
5. Generate a mapping table from the old reference to the new reference using bcftools.

Components

• Tools
  • htslib v1.19.1
  • bcftools v1.19
  • liftover (plugin) v1.20
• Python3 package
  • pandas