GenoSL

Script to genotype single stranded libraries based on forward and reverse read mapping

Usage

Rscript genoSL.R [--] [--help] [--opts OPTS] [--output OUTPUT] [--fasta
       FASTA] input table

Author:

Aida Andrades Valtueña (aida.andrades[at]gmail.com

Description:

Genotypes single stranded libraries based on forward and reverse
mapping reads to account for potential damage

positional arguments:
  input         Path to the snpTable.tsv produced by MultiVCFAnalyzer
  table         Path to table.tsv containing genomes to Genotype. See
                README.md for specific formating

flags:
  -h, --help    show this help message and exit

optional arguments:
  -x, --opts    RDS file containing argument values
  -o, --output  Specify root of output name, default is snpTable
                [default: snpTable]

Input

Table: table.tsv containing genomes to Genotype. The table should be formated as:

sampleName	All	Reverse	Forward
Sample1	Sample1AllReadsVCF	Sample1ReverseReads	Sample1ForwardReads
Sample2	Sample2AllReadsVCF	Sample2ReverseReads	Sample2ForwardReads
Sample3	Sample3AllReadsVCF	Sample3ReverseReads	Sample3ForwardReads

Note: The names specified for each samples must correspond to the column name in the snpTable.tsv produced by MultiVCFAnalyzer