Bcftools filter for presence of info tag9/22/2023 i, -include select sites for which the expression is true (see man page for details) e, -exclude exclude sites for which the expression is true (see man page for details) Un-indexed VCF and BCF and streams will work in most butĪbout: Extracts fields from VCF/BCF file and prints them in user-defined format Most commands accept VCF, bgzipped VCF, and BCF with the file type detectedĪutomatically even when streaming from a pipe. Mpileup multi-way pileup producing genotype likelihoods Gtcheck check sample concordance, detect sample swaps and contamination View VCF/BCF conversion, view, subset and filter VCF/BCF filesĬonsensus create consensus sequence by applying VCF variantsįilter filter VCF/BCF files using fixed thresholds Reheader modify VCF/BCF header, change sample names Query transform VCF/BCF into user-defined formats Merge merge VCF/BCF files files from non-overlapping sample sets Usage: bcftools Ĭoncat concatenate VCF/BCF files from the same set of samplesĬonvert convert VCF/BCF files to different formats and back ![]() Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
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