SNP density script

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SNP density log #SNP-sites v2.3.2 #https://github.com/sanger-pathogens/snp-sites snp-sites -v -o 38.vcf 38_formated.fas Bedtools v2.26.0 bedtools makewindows -g panax_size.txt -w 800 > windows.bed bedtools coverage -a windows.bed -b 38.vcf -counts > snp.density.csv Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR: SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microbial Genomics 2016, 2(4). Quinlan AR: BEDTools: the Swiss‐army tool for genome feature analysis. Current Protocols in Bioinformatics 2014:11.12. 11-11.12. 34.

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