Collection of scripts for bacterial SNP calling
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


Collection of scripts for bacterial SNP calling

Usage: cat merged.vcf | python --use-density --window 1000 --max_snps 3 > merged_nondis.vcf

Usage: python -vcfs vcfs.txt

Where vcfs.txt contains a list of .vcf files.

position,1.vcf,2.vcf,3.vcf,4.vcf 0,0,0,0,0 1000,0,0,0,0 2000,0,0,0,0 3000,0,0,0,0 4000,0,0,0,0 5000,0,0,0,0

Usage: cat merged.vcf | python

This will output a table of allele frequencies, samples v positions extracted from a vcf file containing allele frequencies i.e. VarScan.

sample,14270,17152,18532,19568,19572,32507,36448,60760,64630 sample_900,0,3.85,0,100,100,0,0,76.19,97.87 sample_901,0,0,0,100,100,0,0,72,100 sample_902,0,0,0,100,100,0,0,60,100 sample_903,0,0,0,100,100,0,0,73.33,94.55 sample_910,0,0,0,100,100,0,0,70.97,100 sample_916,0,0,0,100,100,0,0,53.57,88.57 sample_917,0,0,0,100,100,0,0,68.42,96.08 sample_930,0,0,0,100,100,0,0,69.44,94.87 sample_931,0,0,0,100,100,0,0,76.19,93.75