Useful utilities for various variant call manipulations from NGS assembly/alignment results.
Manipulate SNP table from Lasergene results
Filter out SNP calls accordingly. Set SNP % limits and depth boundaries to filter SNPS calls you wish to call as true and change with variantChanger.
snpExtract -snp [0.00 100.00] -depth [0 Inf]
Use the output from snpExtract as input to make SNP changes in original sequence.
variantChanger -seq <sequenceFile> -snp <filteredSNPsFile> -out <outFile