../pipeline/diagrams/snp_parser.blockdiag.txt
The workflow starts with a number of alignments passed to the SNP calling software, which produces one VCF file per alignment/sample. These VCF files are used by SNPDat along a GTF file and the reference genome to integrate the information in VCF files with synonymous/non-synonymous information.
All VCF files are merged into a VCF that includes information about all the SNPs called among all samples. This merged VCF is passed, along with the results from SNPDat and the GFF file to snp_parser.py which integrates information from all data sources and output files in a format that can be later used by the rest of the pipeline.1
Note
The GFF file passed to the parser must have per sample coverage information.
mgkit.workflow.snp_parser
This step is done separately because it's both time consuming and can helps to paralellise later steps↩