When specifying output files explicitly instead v, -verbose produce verbose per-site and per-sample outputĪbout: Converts VCF/BCF to other formats and back. threads number of extra decompression threads u, -user-tstv collect Ts/Tv stats for any tag using the given binning T, -targets-file similar to -R but streams rather than index-jumps t, -targets similar to -r but streams rather than index-jumps S, -samples-file file of samples to include s, -samples list of samples for sample stats, "-" to include all samples R, -regions-file restrict to regions listed in a file r, -regions restrict to comma-separated list of regions I, -split-by-ID collect stats for sites with ID separately (known vs novel) i, -include select sites for which the expression is true (see man page for details) F, - fasta-ref faidx indexed reference sequence file to determine INDEL context f, -apply-filters require at least one of the listed FILTER strings (e.g. E, -exons tab-delimited file with exons for indel frameshifts (chr,from,to 1-based, inclusive, bgzip compressed) e, -exclude exclude sites for which the expression is true (see man page for details) d, -depth depth distribution: min,max,bin size c, -collapse treat as identical records with, see man page for details 1, -1st-allele-only include only 1st allele at multiallelic sites af-tag allele frequency tag to use, by default estimated from AN,AC or GT By default only sites are compared, -s/-S must given to include
When two files are given, the program generates separate stats for intersectionĪnd the complements. Un-indexed VCF and BCF and streams will work in most butĪbout: Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. 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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