bcftools

bcftools is a toolkit for processing and analyzing variant files in VCF, compressed VCF, or BCF format. In this module, bcftools standardizes variant files, applies a basic quality filter, and summarizes raw and filtered variant counts.

Workflow

1. Input variant file
   Upload a VCF, VCF.GZ, or BCF file containing variant records.

2. Standardize input format
   Convert the input file into a compressed VCF format and create an index.

3. Calculate raw variant statistics
   Count total variants, SNPs, INDELs, and sample numbers before filtering.

4. Apply quality filtering
   Filter variants using the default rule QUAL >= 20.

5. Generate filtered statistics
   Output filtered VCF files and summarize raw versus filtered variant counts.

Data

The bcftools sample dataset uses ad-bias.vcf, a small VCF file containing variant records from three samples. It is used to demonstrate VCF standardization, quality-based variant filtering, indexing, and summary statistics generation.

Result

v0.1: The pipeline is stored in Code Repository: CRS1244670077970952192. The computational docker enrionment is stored in Software Repository: SRS1244670812213227520.

Reproducibility

The pipeline utilizes code CRS1244670077970952192 and Docker image SRS1244670812213227520, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'bcftools'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.