spread_and_fix_indels: Prepare input VCF

In andrewGhazi/mpradesigntools: tools for designing MPRA experiments

Description

Prepare an input VCF for sequence generation

Usage

spread_and_fix_indels(vcf_path)

Arguments

vcf_path

path to a vcf to be fixed

Details

This function takes an input vcf, reads it in, spreads any SNPs with alternate alleles across multiple rows, and fixes any indels that are improperly formatted. This means if REF and ALT are listed as "A" and "ATC" they will be replaced with "-" and "TC". If they're "A" and "T,C" this will be spread into two entries of "A" and "T" and "A" and "C".

The output is written to the same directory as the input named "*_fixed.vcf". This is ready to be fed into processVCF()

Value

a data_frame of the fixed VCF

andrewGhazi/mpradesigntools documentation built on Dec. 21, 2020, 3:18 p.m.