Variant calling helpers for handling NGS analysis software results
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README.md
snpExtract.pl
variantChanger.pl

README.md

Varvar

GitHub version Github Issues Pending Pull-Requests GitHub license

Useful utilities for various variant call manipulations from NGS assembly/alignment results.

Lasergene - DNASTAR Software

Manipulate SNP table from Lasergene results

snpExtract

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]

variantChanger

Use the output from snpExtract as input to make SNP changes in original sequence.

variantChanger -seq <sequenceFile> -snp <filteredSNPsFile> -out <outFile

License GitHub license