VCF_PlotKit

Filter & Plot features in VCF files

This package provide tools to work on VCF files.

• Developed by Cecilia Deng (PFR), ...
• Test by JL?

Objectives

• Filter vcf files (SNPs and INDELs) based on various criteria (including homozygous or heteozygous)
• Generate density plot of DP, Mapping quality (MQM, MQMR, or MQ), and QD (quality by depth)
• Generate variant distributions along each chromosomes

Dependencies:

• bcftools
• bgzip/tabix
• R
• PERL

Test done using:

• vcftools/0.1.14
• bedtools/2.21.0
• tabix-0.2.6