md_snv_position: md_snv_position

In shlienlab/ShlienLab.Core.Filter: ShlienLab.Core.Filter

Description

Calculates all the mutated bases and the positions thereof from the information given about a single read. Produces either a data frame of those mutations, or a string detailing why no mutations were found in that specific read.

Usage

md_snv_position(md = NULL, position = NULL, cigar = NULL, seq = NULL, operation = "S")

Arguments

md	String representing an MD tag of a specific read extracted from a BAM file.
position	Number representing the start position of the read (this is adjusted automatically if the read is hard clipped)
cigar	String representing the cigar string of the read, in the correct format.
seq	String representing the sequence of bases in the read (TCAG).
operation	Character representing a CIGAR string operation, either M, I, D, N, S, H, P, =, or X.

Value

Returns either a data frame or a string. If the read does not contain any mutations, returns the string "unmutated". If the read contains either an insertion or deletion in comparison to the reference genome, then this function returns the string "indel". If the read is mutated and does not contain any length differences, then this function returns a data frame with the columns *alt* and *position* which represent the alternative base, and at which position the SNV occurs.

Author(s)

L. Christine Schreiner

shlienlab/ShlienLab.Core.Filter documentation built on May 20, 2019, 5:27 p.m.