NGS-SNP - obtain_INDEL_equivalents_stats.pl

Description

Some INDELs have additional potential functional consequences revealed through equivalent representations, so the true effect cannot be defined with certainty. This script extracts all INDELs with additional consequences and describes the changes in the consequence_change file. The number of potential consequence changes and other summary information are described in a statistics file.

Setup

See setup instructions for NGS-SNP.

Usage

Usage: perl obtain_INDEL_equivalents_stats.pl 
Arguments required:
  -i [FILE] : input indel annotation file (Required).
  -o [FILE] : consequence change output file (Required).
  -s [FILE] : statistics file (Required).
example: perl obtain_INDEL_equivalents_stats.pl -i indels.vcf.annotated -o consequence_changes.txt -s stats.txt
    

Input

An INDEL annotation file as created by the annotate_INDELs.pl script.

Output

This script generates two output files: