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BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
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Uncompressed files are stored in memory, while bgzip-compressed and tabix-indexed region files are streamed. Regions can be specified either on command line or in a VCF, Binary Options BED, or tab-delimited file (the default). To indicate that a file be treated as BED rather than the 1-based tab-delimited file, the file must have the ".bed" or ".bed.gz" suffix (case-insensitive). The columns of the tab-delimited BED file are also CHROM, POS and END (trailing columns are ignored), but coordinates are 0-based, half-open. Note that sequence names must match exactly, "chr20" is not the same as "20". The columns of the tab-delimited file can contain either positions (two-column format) or intervals (three-column format): CHROM, POS, and, optionally, END, where positions are 1-based and inclusive. This option requires indexed VCF/BCF files. Note that -R cannot be used in combination with -r . Note that overlapping regions in FILE can result in duplicated out of order positions in the output. Also note that chromosome ordering in FILE will be respected, the VCF will be processed in the order in which chromosomes first appear in FILE . However, within chromosomes, the VCF will always be processed in ascending genomic coordinate order no matter what order they appear in FILE .
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