With POS at the end of a region, which are technically outside the region) or set Should be included (this is the default behavior of -r/-R, and includes indels Set to record or 1 if also overlapping records with POS outside a region (this corresponds to the default behavior of -t/-T) Set to pos or 0 if the VCF record has to have POS inside a region This option controls how overlapping records are determined: regions-overlap pos| record| variant| 0| 1| 2 This option requires indexed VCF/BCF files. Note that overlapping regions in FILE can result inĭuplicated out of order positions in the output. Processed in ascending genomic coordinate order no matter what order theyĪppear in FILE. However, within chromosomes, the VCF will always be The VCF will be processed in the order in which chromosomes first appear Also note that chromosome ordering in FILE will be respected, Note that sequence names must match exactly, 'chr20' is not the same as Memory, while bgzip-compressed and tabix-indexed region files are streamed. Than the 1-based tab-delimited file, the file must have the '.bed' or To indicate that a file be treated as BED rather The columns of the tab-delimited BED file are alsoĬHROM, POS and END (trailing columns are ignored), but coordinatesĪre 0-based, half-open. (three-column format: CHROM, BEG, END), but not both. The columns of the tab-delimited fileĬan contain either positions (two-column format: CHROM, POS) or intervals Regions can be specified either on command line or in a VCF, BED, or Note that -r cannot be used in combination with -R. Region, unlike the -t/-T options where only the POS coordinate is checked. Records are matched even when the starting coordinate is outside of the r, -regions chr| chr:pos| chr:beg-end| chr:beg-Ĭomma-separated list of regions, see also -R, -regions-file. The compression level of the compressed formats ( b and z) can be set byīy appending a number between 0-9. Performance by removing unnecessary compression/decompression and Use the -Ou option when piping between bcftools subcommands to speed up Output compressed BCF ( b), uncompressed BCF ( u), compressed VCF ( z), uncompressed VCF ( v). The file type is determined automatically from the file name suffix and inĬase a conflicting -O option is given, the file name suffix takes precedence. To standard output, where it is written by default. When output consists of a single stream, write it to FILE rather than For example, to include only sites which have no filters set,ĭo not append version and command line information to the output VCF header. Skip sites where FILTER column does not contain any of the strings listed Only records with identical ID column are compatible. For duplicate positions, only theįirst indel record will be considered and appear on output. indelsĪll indel records are compatible, regardless of whether the REFĪnd ALT alleles match or not. Record will be considered and appear on output. For duplicate positions, only the first SNP snpsĪny SNP records are compatible, regardless of whether the ALTĪlleles match or not. The first will be considered and appear on output. In the case of records with the same position, only Only records where some subset of ALT alleles match are compatible allĪll records are compatible, regardless of whether the ALT alleles Only records with identical REF and ALT alleles are compatible some

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