Variant calling with SNIPPY

Manuals

• SNIPPY manual
• BWA manual
• samtools
• FreeBayes
• bcftools

Getting reference data

• NCBI Ecoli ST38

Practicals - single genome:

1. Create a directory to work in, and go into it
2. Copy data from reference site:

     cp -r /projects/nn9305k/bioinf_course/variantcalling/snippy .
   

3. Look to see what contents are in the various directories (analysis is pre-cooked)
4. Run a simple analysis, with one isolate against the reference
   • Create a screen
   • Set up a qlogin
   • activate snippy 4, with conda (conda activate snippy4)
   • Run a single genome
5. While it is running, try to identify what commands that is being run. We will dissect them one by one.
6. Look at output files, and see what they are - compare to SNIPPY webpage.
7. How to look at bam files:

   • samtools view snps.bam

     less

     • find name of contig, second column
   • samtools tview snsps.bam reference/ref.fa
   • use q to get a search field, input contig name

Practicals - run with multiple genomes

SNIPPY can also run multiple genomes against the same reference. This is done with the snippy-multi option. As input to that, we create a list of genomes as seen in list.txt.

We can use this as input to a snippy-multi run. A sample result from such a run can be found in the analysis directory.