'\" t

.TH annot-tsv 1 "15 April 2024" "htslib-1.20" "Bioinformatics tools"

.\"

.\" Copyright (C) 2015, 2017-2018, 2023-2024 Genome Research Ltd.

.\"

.\" Author: Petr Danecek

.\"

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.\" For code blocks and examples (cf groff's Ultrix-specific man macros)

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.SH NAME

annot\-tsv \- transfer annotations from one TSV (tab\-separated values) file into another

.SH SYNOPSIS

.PP

.B annot-tsv

.RI [ OPTIONS ]

.SH DESCRIPTION

The program finds overlaps in two sets of genomic regions (for example two CNV call sets) and annotates regions of the target file

.RB ( \-t ", " \-\-target\-file )

with information from overlapping regions of the source file

.RB ( \-s ", " \-\-source\-file ).

It can transfer one or multiple columns

.RB ( \-f ", " \-\-transfer )

and the transfer can be conditioned on requiring matching values in one or more columns

.RB ( \-m ", " \-\-match ).

In addition to column transfer

.RB ( \-f )

and special annotations

.RB ( \-a ", " \-\-annotate ),

the program can operate in a simple grep-like mode and print matching lines (when neither

.B \-f

nor

.B \-a

are given) or drop matching lines

.RB ( \-x ", " \-\-drop-overlaps ).

All indexes and coordinates are 1-based and inclusive.

.SH OPTIONS

.SS "Common Options"

.PP

.BR \-c ", " \-\-core " SRC:TGT"

.RS 4

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 instead (for example "chr,beg,end:3,1,2").

Note that regions are not required, the program can work with a list of positions (for example "chr,beg,end:CHROM,POS,POS").

.RE

.PP

.BR \-f ", " \-\-transfer " SRC:TGT"

.RS 4

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.

.RE

.PP

.BR \-m ", " \-\-match " SRC:TGT"

.RS 4

The columns required to be identical

.RE

.PP

.BR \-o ", " \-\-output " FILE"

.RS 4

Output file name, by default the result is printed on standard output

.RE

.PP

.BR \-s ", " \-\-source\-file " FILE"

.RS 4

Source file with annotations to transfer

.RE

.PP

.BR \-t ", " \-\-target\-file " FILE"

.RS 4

Target file to be extend with annotations from

.BR \-s ", " \-\-source\-file

.RE

.SS "Other options"

.PP

.B \-\-allow\-dups

.RS 4

Add the same annotations multiple times if multiple overlaps are found

.RE

.PP

.B \-\-help

.RS 4

This help message

.RE

.PP

.BR \-\-max\-annots " INT"

.RS 4

Add at most INT annotations per column to save time when many overlaps are found with a single region

.RE

.PP

.B \-\-version

.RS 4

Print version string and exit

.RE

.PP

.BR \-a ", " \-\-annotate " LIST"

.RS 4

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.

.PP

.I cnt

.RS 4

number of overlapping regions

.RE

.PP

.I frac

.RS 4

fraction of the target region with an overlap

.RE

.PP

.I nbp

.RS 4

number of source base pairs in the overlap

.RE

.RE

.PP

.BR \-d ", " \-\-delim " SRC:TGT"

.RS 4

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'".

.RE

.PP

.BR \-h ", " \-\-headers " SRC:TGT"

.RS 4

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 equivalent 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).

.RE

.PP

.BR \-H ", " \-\-ignore\-headers

.RS 4

Ignore the headers completely and use numeric indexes even when a header exists

.RE

.PP

.BR \-I ", " \-\-no\-hdr\-idx

.RS 4

Suppress index numbers in the printed header. If given twice, drop the entire header.

.RE

.PP

.BR \-O ", " \-\-overlap " FLOAT"

.RS 4

Minimum overlap as a fraction of region length in at least one of the overlapping regions. If also

.BR \-r ", " \-\-reciprocal

is given, require at least

.I FLOAT

overlap with respect to both regions

.RE

.PP

.BR \-r ", " \-\-reciprocal

.RS 4

Require the

.BR \-O ", " \-\-overlap

with respect to both overlapping regions

.RE

.PP

.BR \-x ", " \-\-drop-overlaps

.RS 4

Drop overlapping regions (cannot be combined with

.BR \-f ", " \-\-transfer )

.RE

.SH EXAMPLE

Both SRC and TGT input files must be tab-delimited files with or without a header, their columns can be named differently, can appear in arbitrary order. For example consider the source file

.EX

#chr beg end sample type qual

chr1 100 200 smpl1 DEL 10

chr1 300 400 smpl2 DUP 30

.EE

and the target file

.EX

150 200 chr1 smpl1

150 200 chr1 smpl2

350 400 chr1 smpl1

350 400 chr1 smpl2

.EE

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

.EX

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

.EE

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:

.EX

#from to chrom sample

150 200 chr1 smpl1

150 200 chr1 smpl2

350 400 chr1 smpl1

350 400 chr1 smpl2

.EE

.EX

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

.EE

One of the SRC or TGT file can be streamed from stdin

.EX

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

.EE

The program can be used in a grep-like mode to print only matching regions of the target file without modifying the records

.EX

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

.EE

.SH AUTHORS

The program was written by Petr Danecek and was originally published on github as annot\-regs

.SH COPYING

The MIT/Expat License, see the LICENSE document for details.

.br

Copyright (c) Genome Research Ltd.