42 lines
3.0 KiB
Plaintext
42 lines
3.0 KiB
Plaintext
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```
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bcftools annotate -h
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```
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annotate: option requires an argument -- 'h'
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About: Annotate and edit VCF/BCF files.
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Usage: bcftools annotate [options] VCF
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Options:
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-a, --annotations FILE VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+
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-c, --columns LIST List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details
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-C, --columns-file FILE Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE]
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-e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)
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--force Continue despite parsing error (at your own risk!)
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-H, --header-line STR Header line which should be appended to the VCF header, can be given multiple times
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-h, --header-lines FILE Lines which should be appended to the VCF header
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-I, --set-id [+]FORMAT Set ID column using a `bcftools query`-like expression, see man page for details
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-i, --include EXPR Select sites for which the expression is true (see man page for details)
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-k, --keep-sites Leave -i/-e sites unchanged instead of discarding them
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-l, --merge-logic TAG:TYPE Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL
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-m, --mark-sites [+-]TAG Add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the -a file
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--min-overlap ANN:VCF Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF)
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--no-version Do not append version and command line to the header
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-o, --output FILE Write output to a file [standard output]
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-O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
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--pair-logic STR Matching records by <snps|indels|both|all|some|exact>, see man page for details [some]
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-r, --regions REGION Restrict to comma-separated list of regions
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-R, --regions-file FILE Restrict to regions listed in FILE
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--regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
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--rename-annots FILE Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT
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--rename-chrs FILE Rename sequences according to the mapping: old\tnew
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-s, --samples [^]LIST Comma separated list of samples to annotate (or exclude with "^" prefix)
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-S, --samples-file [^]FILE File of samples to annotate (or exclude with "^" prefix)
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--single-overlaps Keep memory low by avoiding complexities arising from handling multiple overlapping intervals
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-x, --remove LIST List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with "^" prefix). See man page for details
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--threads INT Number of extra output compression threads [0]
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Examples:
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http://samtools.github.io/bcftools/howtos/annotate.html
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