Barcoding tools

Process

The Barcoding tools are a little different from the other tools in that the do not access the BAM file directly, but rather they use VCFs which are created from BAM files from other tools. Hence the process is as follows:

1. For each sample, we run samtools mpileup to create a VCF file containing the allele read depths at each SNP in a master list (the SNPs we want in the barcode)
2. We then run the Barcoding tools to use the read counts in the VCFs to produce genotypes and then concatenate them in the desired order to form barcodes.