prepare.bam.specification {varitas}

Prepare BAM specification data frame to standardized format for downstream analyses.

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