What it does

Create the SNP matrix containing the consensus base for each of the samples at the positions where high-confidence SNPs were found in any of the samples. The matrix contains one row per sample and one column per SNP position. Non-SNP positions are not included in the matrix. The matrix is formatted as a fasta file, with each sequence (all of identical length) corresponding to the SNPs in the correspondingly named sequence.

More information

CFSAN SNP Pipeline create SNP matrix documentation