# 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](https://www.medrxiv.org/content/10.1101/2021.11.12.21266253v1) 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.
```bash
git clone https://github.com/Illumina/Gauchian
cd Gauchian
python3 setup.py install
```
## Running the program
```bash
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|
Raw data
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"description": "# Gauchian: WGS-based GBA variant caller\n\nGauchian 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](https://www.medrxiv.org/content/10.1101/2021.11.12.21266253v1) for more details about the method.\n\n## Installation\n\nThis Python package is supported for Linux and macOS. It has been tested on CentOS 7.9.2009.\n\nThe Python dependencies can be found in `requirements.txt`. Installation takes a few seconds.\n\n```bash\ngit clone https://github.com/Illumina/Gauchian\ncd Gauchian\npython3 setup.py install\n```\n\n## Running the program\n\n```bash\ngauchian --manifest MANIFEST_FILE \\\n --genome [19/37/38] \\\n --prefix OUTPUT_FILE_PREFIX \\\n --outDir OUTPUT_DIRECTORY \\\n --threads NUMBER_THREADS\n```\n\nThe 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.\n\nFor CRAM input, it\u2019s suggested to provide the path to the reference fasta file with `--reference` in the command.\n\n## Interpreting the output\n\nThe program produces a .tsv file in the directory specified by --outDir.\nThe fields are explained below:\n\n| Fields in tsv | Explanation |\n|:-----------------------------------------|:-------------------------------------------------------------------------------|\n| Sample | Sample name |\n| is_biallelic(GBAP1-like_variant_exon9-11)| Whether the sample is called as biallelic for GBAP1-like variants in exon9-11 |\n| is_carrier(GBAP1-like_variant_exon9-11) | Whether the sample is called as a carrier for GBAP1-like variants in exon9-11 |\n| CN(GBA+GBAP1) | Total copy number of GBA+GBAP1 |\n| deletion_breakpoint_in_GBA | Whether the deletion breakpoint is in GBA gene if a deletion exists |\n| GBAP1-like_variant_exon9-11 | GBAP1-like variants called in exon9-11, two alleles separated by / |\n| other_unphased_variants | Other variants called (non-GBAP1-like variants or variants outside of exon9-11)|\n\nA .json file is also produced that contains more information about each sample.\n\n| Fields in json | Explanation |\n|:------------------|:----------------------------------------------------------------------------------|\n| Coverage_MAD | Median absolute deviation of depth, measure of sample quality |\n| Median_depth | Sample median depth |\n| deletion_CN | CN of the unique region between GBA and GBAP1. This value plus 2 is the total CN |\n| deletion_CN_raw | Raw normalized depth of the unique region between GBA and GBAP1 |\n| variant_raw_count | Supporting reads for each variant |\n| snp_call | GBA copy number call at GBA/GBAP1 differentiating sites |\n| snp_raw | Raw GBA copy number at GBA/GBAP1 differentiating sites |\n| haplotypes | Summary of haplotypes assembled across GBA/GBAP1 differentiating sites in Exon9-11|\n\n\n",
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