Collection of scripts for bacterial SNP calling
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README.md
count_snp_density.py
filter_non_discriminatory_variants.py
find_islands.py
output_af_from_vcf.py
plot_density.R
qc_vcf.py

README.md

snp_calling_scripts

Collection of scripts for bacterial SNP calling

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


Usage: python count_snp_density.py -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 output_af_from_vcf.py

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