bio-variant-calling - Variant Calling with bcftools from BAM Alignments
Detect SNPs and indels from aligned reads using bcftools mpileup and call pipeline, generating VCF output from BAM files.
Tags
Updated: 2026-06-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Call SNPs and indels from BAM
- Generate pileup from aligned reads
- Call variants for specific regions
- Call variants from multiple BAMs
- Annotate variants with read depth
- Set ploidy for variant calling
- Output compressed VCF files
- Index VCF output files
- Parallelize calling by chromosome
- Concatenate per-chromosome VCF results
Inputs
- BAM file(s)
- Reference FASTA file
- Target regions BED file
- BAM list file
- Ploidy configuration file
Outputs
- VCF variant file
- Compressed VCF file
- VCF index file
Requirements
- bcftools 1.19 or later
- BAM file aligned to matching reference
- BAM file must be indexed