prepare.bam.specification: Prepare BAM specification data frame to standardized format...

In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description

This function prepares a data frame that can be used to run variant callers. For matched normal variant calling, this data frame will contain three columns with names: sample.id, tumour.bam, normal.bam For unpaired variant calling, the data frame will contain two columns with names: sample.id, tumour.bam

Usage

prepare.bam.specification(sample.details, paired = TRUE,
  sample.id.column = 1, tumour.bam.column = 2, normal.bam.column = 3)

Arguments

sample.details	Data frame where each row represents a sample to be run. Must contain sample ID, path to tumour BAM, and path to normal BAM.
paired	Logical indicating whether the sample specification is for a paired analysis.
sample.id.column	Index or string giving column of sample.details that contains the sample ID
tumour.bam.column	Index or string giving column of sample.details that contains the path to the tumour BAM
normal.bam.column	Index or string giving column of sample.details that contains the path to the normal BAM

Value

bam.specification Data frame with one row per sample to be run

varitas documentation built on Nov. 14, 2020, 1:07 a.m.