remove_vcf_info_fields's Introduction

remove_vcf_info_fields

Remove one or more INFO fields from a VCF file.

Installation/Requirements

Python3 and the modules 'parse_vcf' is required. The 'biopython' module is required to write BGZIP compressed output. To install via pip run:

pip3 install parse_vcf
pip3 install biopython

Usage

usage: remove_info_fields.py [-h] -i VCF_INPUT [-o OUTPUT]
                             (-r REMOVE_FIELDS [REMOVE_FIELDS ...] | -k KEEP_FIELDS [KEEP_FIELDS ...])

Remove specific INFO fields from a VCF file.

optional arguments:
  -h, --help            show this help message and exit
  -i VCF_INPUT, --vcf_input VCF_INPUT, --vcf VCF_INPUT
                        Input VCF file
  -o OUTPUT, --output OUTPUT
                        Output VCF file. If the given filename ends with '.gz'
                        or '.bgz' the output will be written compressed via
                        BGZIP.
  -r REMOVE_FIELDS [REMOVE_FIELDS ...], --remove_fields REMOVE_FIELDS [REMOVE_FIELDS ...]
                        One or more INFO fields to remove.
  -k KEEP_FIELDS [KEEP_FIELDS ...], --keep_fields KEEP_FIELDS [KEEP_FIELDS ...]
                        One or more INFO fields to retain. All other INFO
                        fields will be removed as long as they are defined in
                        the VCF header.

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