These scripts are part of hits pipeline for DNA resequencing, which are used to identify sector variant.
Usage: filter_vcf.pl vcf_file <DP> <IMF> <AF1> <DP4>
e.g.: filter_vcf.pl sector.vcf 20 0.85 0.90 0.80
Usage: ./vcfcmp ref.vcf var1.vcf var2.vcf ...
e.g.: ./vcfcmp WT.vcf MU.vcf
- For Sclerotinia sclerotiorum, use vcfcmp.ss and filter_vcf.ss.pl, please.
Qinhu Wang (wangqinhu@nwafu.edu.cn)
2017 (c) Xu Lab, Northwest A&F University
MIT