vcfc's Introduction

vcfc 🧬

A C library and programs for working with VCF files

Build from GitHub 💾

git clone https://github.com/alexcoppe/vcfc.git
cd vcfc
make

Programs available 👨‍💻

get_columns2

Shows only the columns you choose from a multi columns file (usually named cvs file). You have to choose the columns by numbers using the -f parameter. It works on a .vcf file and does not shows meta-information lines e.g. ##fileformat=VCFv4.2.

Option	What does it do
-h	Show help
-d	The field delimiter to use instead of the tab character
-f	The fields to be shown (separated by ,)

Example

>>> get_columns2   -f 2,1,3,4  input.txt

get_pass_variants

This program filters a VCF file showing only the ones with PASS (annotated by SnpEff) in the FILTER field.

Option	What does it do
-h	Show help

Example

>>> get_pass_variants mutations.vcf

filter_vcf_by_bed

Filter a VCF file using a BED file.

Option	What does it do
-h	Show help
-a	show the header in the filtered VCF

>>> filter_vcf_by_bed -a sample.bed variants.vcf

Functions available 📚:

The following table shows the available functions. If you want to see a detailed description of the functions go to the library documentation page.

Function	Description
bed_entries	reads a file and returns an array of BedEntry pointers. Use a single free call to free the array
get_format_fields	takes as input a pointer to a format string (var->format) or a sample string (like var->samples[0]) gotten from the Variant struct and returns an array of pointers to the format or sample fields
get_variant_from_vcf_line	reads a single line from a VCF file and returns a Variant struct
free_variant	frees the memory allocatated by the get_variant_from_vcf_line
nice_print_variant	prints all the fields from a Variant struct

Recommend Projects