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annot-tsv(1) Bioinformatics tools annot-tsv(1) NAME annot-tsv - transfer annotations from one TSV (tab-separated values) file into another SYNOPSIS annot-tsv [OPTIONS] DESCRIPTION The program finds overlaps in two sets of genomic regions (for example two CNV call sets) and annotates regions of the target file (-t, --tar- get-file) with information from overlapping regions of the source file (-s, --source-file). It can transfer one or multiple columns (-f, --transfer) and the trans- fer can be conditioned on requiring matching values in one or more columns (-m, --match). In addition to column transfer (-f) and special annotations (-a, --annotate), the program can operate in a simple grep- like mode and print matching lines (when neither -f nor -a are given) or drop matching lines (-x, --drop-overlaps). All indexes and coordinates are 1-based and inclusive. OPTIONS Common Options -c, --core SRC:TGT List of names of the core columns, in the order of chromosome, start and end positions, irrespective of the header name and order in which they appear in source or target files (for example "chr,beg,end:CHROM,START,END"). If both files use the same header names, the TGT names can be omitted (for example "chr,beg,end"). If SRC or TGT file has no header, 1-based indexes can be given in- stead (for example "chr,beg,end:3,1,2"). Note that regions are not required, the program can work with a list of positions (for exam- ple "chr,beg,end:CHROM,POS,POS"). -f, --transfer SRC:TGT Comma-separated list of columns to transfer. If the SRC column does not exist, interpret it as the default value to fill in when a match is found or a dot (".") when a match is not found. If the TGT column does not exist, a new column is created. If the TGT column already exists, its values will be overwritten when overlap is found and left as is otherwise. -m, --match SRC:TGT The columns required to be identical -o, --output FILE Output file name, by default the result is printed on standard out- put -s, --source-file FILE Source file with annotations to transfer -t, --target-file FILE Target file to be extend with annotations from -s, --source-file Other options --allow-dups Add the same annotations multiple times if multiple overlaps are found --help This help message --max-annots INT Add at most INT annotations per column to save time when many over- laps are found with a single region --version Print version string and exit -a, --annotate LIST Add one or more special annotation and its target name separated by ':'. If no target name is given, the special annotation's name will be used in output header. cnt number of overlapping regions frac fraction of the target region with an overlap nbp number of source base pairs in the overlap -d, --delim SRC:TGT Column delimiter in the source and the target file. For example, if both files are comma-delimited, run with "--delim ,:," or simply "--delim ,". If the source file is comma-delimited and the target file is tab-delimited, run with "-d $',:\t'". -h, --headers SRC:TGT Line number of the header row with column names. By default the first line is interpreted as header if it starts with the comment character ("#"), otherwise expects numeric indices. However, if the first line does not start with "#" but still contains the column names, use "--headers 1:1". To ignore existing header (skip comment lines) and use numeric indices, use "--headers 0:0" which is equiv- alent to "--ignore-headers". When negative value is given, it is interpreted as the number of lines from the end of the comment block. Specifically, "--headers -1" takes the column names from the last line of the comment block (e.g., the "#CHROM" line in the VCF format). -H, --ignore-headers Ignore the headers completely and use numeric indexes even when a header exists -I, --no-hdr-idx Suppress index numbers in the printed header. If given twice, drop the entire header. -O, --overlap FLOAT,[FLOAT] Minimum overlap as a fraction of region length in SRC and TGT, re- spectively (with two numbers), or in at least one of the overlap- ping regions (with a single number). If also -r, --reciprocal is given, require at least FLOAT overlap with respect to both regions. Two identical numbers are equivalent to running with -r, --recipro- cal -r, --reciprocal Require the -O, --overlap with respect to both overlapping regions -x, --drop-overlaps Drop overlapping regions (cannot be combined with -f, --transfer) EXAMPLE Both SRC and TGT input files must be tab-delimited files with or with- out a header, their columns can be named differently, can appear in ar- bitrary order. For example consider the source file #chr beg end sample type qual chr1 100 200 smpl1 DEL 10 chr1 300 400 smpl2 DUP 30 and the target file 150 200 chr1 smpl1 150 200 chr1 smpl2 350 400 chr1 smpl1 350 400 chr1 smpl2 In the first example we transfer type and quality but only for regions with matching sample. Notice that the header is present in SRC but not in TGT, therefore we use column indexes for the latter annot-tsv -s src.txt.gz -t tgt.txt.gz -c chr,beg,end:3,1,2 -m sample:4 -f type,qual 150 200 chr1 smpl1 DEL 10 150 200 chr1 smpl2 . . 350 400 chr1 smpl1 . . 350 400 chr1 smpl2 DUP 30 The next example demonstrates the special annotations nbp and cnt, with target name as pair,count. In this case we use a target file with headers so that column names will be copied to the output: #from to chrom sample 150 200 chr1 smpl1 150 200 chr1 smpl2 350 400 chr1 smpl1 350 400 chr1 smpl2 annot-tsv -s src.txt.gz -t tgt_hdr.txt.gz -c chr,beg,end:chrom,from,to -m sample -f type,qual -a nbp,cnt:pair,count #[1]from [2]to [3]chrom [4]sample [5]type [6]qual [7]pair [8]count 150 200 chr1 smpl1 DEL 10 51 1 150 200 chr1 smpl2 . . 0 0 350 400 chr1 smpl1 . . 0 0 350 400 chr1 smpl2 DUP 30 51 1 One of the SRC or TGT file can be streamed from stdin cat src.txt | annot-tsv -t tgt.txt -c chr,beg,end:3,2,1 -m sample:4 -f type,qual -o output.txt cat tgt.txt | annot-tsv -s src.txt -c chr,beg,end:3,2,1 -m sample:4 -f type,qual -o output.txt The program can be used in a grep-like mode to print only matching re- gions of the target file without modifying the records annot-tsv -s src.txt -t tgt.txt -c chr,beg,end:3,2,1 -m sample:4 150 200 chr1 smpl1 350 400 chr1 smpl2 AUTHORS The program was written by Petr Danecek and was originally published on github as annot-regs COPYING The MIT/Expat License, see the LICENSE document for details. Copyright (c) Genome Research Ltd. htslib-1.21 12 September 2024 annot-tsv(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLE | AUTHORS | COPYING
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