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bcftools view (version 1.0.0)

Choose a bcf file to view:

Retain all possible alternate alleles at variant sites:

Output in the BCF format. The default is VCF.:

Sequence dictionary (list of chromosome names) for VCF->BCF conversion.:

Indicate PL is generated by r921 or before (ordering is different).:

Suppress all individual genotype information.:

Skip sites where the REF field is not A/C/G/T:

The input is VCF instead of BCF.:

Uncompressed BCF output.:

Call variants using Bayesian inference. Automatically performs max-likelihood inference only:

Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT.:

Call per-sample genotypes at variant sites:

Use alternate INDEL-to-SNP mutation rate, default 0.15.:

variant_filter:

Specify scaled mutation rate for variant calling, default is 0.001.:

Output variant sites only.: