gauchian 1.0.2

WGS-based GBA variant caller

Gauchian: WGS-based GBA variant caller

Gauchian is a targeted variant caller for the GBA gene based on a whole-genome sequencing (WGS) BAM file. Gauchian uses a novel method to solve the problems caused by the high sequence similarity with the pseudogene paralog GBAP1 and is able to detect variants accurately in the Exons 9-11 homology region, such as large deletions or duplications between GBA and GBAP1, and GBAP1-like variants in GBA, including p.A495P, p.L483P, p.D448H, c.1263del, RecNciI, RecTL and c.1263del+RecTL. In addition to these challenging variants, Gauchian also calls known pathogenic or likely pathogenic GBA variants classified in ClinVar. Gauchian has been tested on Illumina WGS data with standard sequencing depth (>=30X). Gauchian does not work on targeted sequencing data. Please refer to our preprint for more details about the method.

Installation

This Python package is supported for Linux and macOS. It has been tested on CentOS 7.9.2009.

The Python dependencies can be found in requirements.txt. Installation takes a few seconds.

git clone https://github.com/Illumina/Gauchian
cd Gauchian
python3 setup.py install

Running the program

gauchian --manifest MANIFEST_FILE \
         --genome [19/37/38] \
         --prefix OUTPUT_FILE_PREFIX \
         --outDir OUTPUT_DIRECTORY \
         --threads NUMBER_THREADS

The manifest is a text file in which each line should list the absolute path to an input WGS BAM/CRAM file. Full WGS BAM/CRAM files are recommended. If you would like to use a subsetted bamlet, please subset using region files in gauchian/data/GBA_region_*.bed.

For CRAM input, it’s suggested to provide the path to the reference fasta file with --reference in the command.

Interpreting the output

The program produces a .tsv file in the directory specified by --outDir. The fields are explained below:

Fields in tsv	Explanation
Sample	Sample name
is_biallelic(GBAP1-like_variant_exon9-11)	Whether the sample is called as biallelic for GBAP1-like variants in exon9-11
is_carrier(GBAP1-like_variant_exon9-11)	Whether the sample is called as a carrier for GBAP1-like variants in exon9-11
CN(GBA+GBAP1)	Total copy number of GBA+GBAP1
deletion_breakpoint_in_GBA	Whether the deletion breakpoint is in GBA gene if a deletion exists
GBAP1-like_variant_exon9-11	GBAP1-like variants called in exon9-11, two alleles separated by /
other_unphased_variants	Other variants called (non-GBAP1-like variants or variants outside of exon9-11)

A .json file is also produced that contains more information about each sample.

Fields in json	Explanation
Coverage_MAD	Median absolute deviation of depth, measure of sample quality
Median_depth	Sample median depth
deletion_CN	CN of the unique region between GBA and GBAP1. This value plus 2 is the total CN
deletion_CN_raw	Raw normalized depth of the unique region between GBA and GBAP1
variant_raw_count	Supporting reads for each variant
snp_call	GBA copy number call at GBA/GBAP1 differentiating sites
snp_raw	Raw GBA copy number at GBA/GBAP1 differentiating sites
haplotypes	Summary of haplotypes assembled across GBA/GBAP1 differentiating sites in Exon9-11