vcf2seq 0.9.5

Inputing a VCF file, it returns the genomic sequence at the specified length (31 by default).

vcf2seq

Aim

Similar to seqtailor [PMID:31045209] : reads a VCF file, outputs a genomic sequence (default length: 31)

Unlike seqtailor, all sequences will have the same length. Moreover, it is possible to have an absence character (by default the dot . ) for indels.

• When a insertion is larger than --size parameter, only first --size nucleotides are outputed.
• Sequence headers are formated as "_".

VCF format specifications: https://github.com/samtools/hts-specs/blob/master/VCFv4.4.pdf

Installation

pip install vcf2seq

usage

usage: vcf2seq.py [-h] -g genome [-s SIZE] [-t {alt,ref,both}] [-b BLANK] [-a ADD_COLUMNS [ADD_COLUMNS ...]] [-o OUTPUT] [-v] vcf


positional arguments:
  vcf                   vcf file (mandatory)

options:
  -h, --help            show this help message and exit
  -g genome, --genome genome
                        genome as fasta file (mandatory)
  -s SIZE, --size SIZE  size of the output sequence (default: 31)
  -t {alt,ref,both}, --type {alt,ref,both}
                        alt, ref, or both output? (default: alt)
  -b BLANK, --blank BLANK
                        Missing nucleotide character, default is dot (.)
  -a ADD_COLUMNS [ADD_COLUMNS ...], --add-columns ADD_COLUMNS [ADD_COLUMNS ...]
                        Add one or more columns to header (ex: '-a 3 AA' will add columns 3 and 27). The first column is '1' (or 'A')
  -o OUTPUT, --output OUTPUT
                        Output file (default: <input_file>-vcf2seq.fa/tsv)
  -f {fa,tsv}, --output-format {fa,tsv}
                        Output file format (default: fa)
  -v, --version         show program's version number and exit