vcf2vcf.py - manipulate vcf files¶

Purpose¶

Manipulate vcf-formatted files.

Usage¶

Type:

python vcf2vcf.py --help

for command line usage.

This script provides the following methods:

re-order: reorder sample columns in vcf formatted file according to a given sort order

cgat.tools.vcf2vcf.Documentation()¶

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This is a tool for manipulating vcf-formatted files. The following

options are available:

+-----------+-------------------------+

+-----------+-------------------------+

lift-over

^^^^^^^^^

Command line options

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usage: vcf2vcf [-h] [--version] [--input-filename-fasta INPUT_FILENAME_FASTA]
               [--input-filename-bam INPUT_FILENAME_BAM]
               [--method {add-strelka-genotype,lift-over}]
               [--input-filename-chain INPUT_FILENAME_CHAIN]
               [--normal-sample-regex NORMAL_SAMPLE_REGEX]
               [--output-filename-unmapped OUTPUT_FILENAME_UNMAPPED]
               [--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
               [--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
               [--log-config-filename LOG_CONFIG_FILENAME]
               [--tracing {function}] [-? ?] [-P OUTPUT_FILENAME_PATTERN] [-F]
               [-I STDIN] [-L STDLOG] [-E STDERR] [-S STDOUT]
vcf2vcf: error: argument -?: expected one argument