higlass-data

Package that creates data files for CGAP's Higlass browsers

Installation

Simply run pip install cgap-higlass-data to install the package. You need at least Python 3.8.

To develop this package, clone this repo, make sure poetry is installed on your system and run make install.

Commands

After installation the following commands can be run from the command line:

Convert BED file to BW (bigWig) file

Assume you have a BED file of the form

# HEADER LINE 1
# HEADER LINE 2
chr1	0	1024	.	423
chr1	1024	2048	.	32
chr1	2048	3072	.	734

This BED file can be converted to a BW file with the following command

# -i input BED file path
# -o output BW file path
# -a assembly (currently only 'hg38' is supported
# -l number of header lines in the BED file
convert-bed-to-bw -i ./PATH/input.bed \
                  -o ./PATH/output.bw \
                  -a hg38 \
                  -l 2

Note that the bedGraphToBigWig must be installed on your system for this to work. It can be installed via conda (conda install -c bioconda ucsc-bedgraphtobigwig). You can also download the binary here: http://hgdownload.soe.ucsc.edu/admin/exe/

Create variant-level VCF for CGAP's cohort browser

This command creates a multiresolution VCF file that is compatible to CGAP's cohort browser. Typically, the input VCF will be VEP annotated and has at least the info field level_most_severe_consequence (which is one of HIGH, LOW, MODERATE, MODIFIER) and an importance value that can ranks/sorts the variants. The info field that is used for that purpose can be set dynamically.

# -i input VCF path
# -o output VCF path
# -c info field in the input VCF that ranks the variants
# -m maximal tile values per consequence. Controls how may variants are displayed at once and a certain zoom level
# -q quiet True / False. Toggles verbose output
# -w chromosome-wise True / False. Significantly less memory intensive, but slightly slower.
# -t index output. True / False. If true, the output vcf will be indexed.
create-cohort-vcf -i ./PATH/input.vcf \
                  -o ./PATH/output.vcf \
                  -c p_value_negative_log_10 \
                  -q True

Create coverage BED file from VCF

Counts the number of variants in a 1024bp window and creates a BED file with the results.

# -i input VCF path
# -o output VCF path
# -a assembly
# -q quiet True / False. Toggles verbose output
create-coverage-bed -i ./PATH/input.vcf \
                    -o ./PATH/output.bed \
                    -a hg38 \
                    -q True