BCFTOOLS CALL

Perform SNP and indel calling from genotype likelihoods

BCFTOOLS CALL

Function

bcftools call performs SNP and indel calling from genotype likelihoods generated by bcftools mpileup.

Input Format

  • BCF files (.bcf) from mpileup
  • Sorted and indexed inputs recommended
  • Supports diploid, haploid, and polyploid data

Output Format

  • VCF (.vcf.gz)
  • BCF (.bcf)
  • Genotype calls with quality scores

Applications

  • SNP detection
  • Indel calling
  • Multi-sample variant calling
  • Consensus generation
  • Population-scale analysis

Example Usage

bcftools call -mv input.bcf -Oz -o output.vcf.gz
bcftools call -cv input.bcf -Ob -o output.bcf
bcftools call -mv --ploidy 2 input.bcf -Oz -o output.vcf.gz
bcftools call -mv -r chr1:1000-5000 input.bcf -Oz -o region.vcf.gz
Important Notes:
  • Use -m for multiallelic calling (recommended).
  • Ensure correct ploidy for accurate results.
  • Input must be generated using bcftools mpileup.
  • Region queries require indexed files.