Snippy @VERSION@
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
Author
Torsten Seemann
Inputs
- NGS Reads in fastq format (single or paired end)
- Reference file in either fasta or genbank format
If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.
Advanced options
- mapping quality - Integer - Minimum mapping quality to allow (default '60')
- minimum coverage - Integer - Minimum coverage of variant site (default '10')
- minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
- minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
- rgid - String - Use this @RG ID: in the BAM header (default '')
- bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
Further information
For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy