simplify_variant: simplify_variant

In ahopki14/vai: Package to annotate VCF files with info from ExAC Database

Description

Removes extraneous bases from variants after mult-allelic variants have been expanded in a VCF file. This function only fixes the REF and ALT fields of the @geno slot as well as the rownames (containing the variant name in the format chr:pos_ref/alt). The position component of the variant name is also corrected appropriately.

Usage

simplify_variant(x)

Arguments

x	A single row of a expanded VCF object (optionally) needing to be simplified

Value

A VCF object of length 1, with the REF, ALT and rowname simplified

Note

As an example, the variant chr1:123456_GC/GA is simplified to chr1:123457_C/A

Author(s)

Alexander Hopkins

References

http://www.cureffi.org/2014/04/24/converting-genetic-variants-to-their-minimal-representation/

ahopki14/vai documentation built on May 25, 2019, 2:25 p.m.