SNP Filtering Metrics from VCF

Question

[StarCute]

I have two VCF files. One was generated using Samtools mpileup and the other Freebayes. I would like to do an intersection of these two VCF files and combine them using VCFtools. I want to filter SNPs based on their quality score, but do not know of a good way to choose the quality score value to filter on for my data.

What is a general guideline for choosing the quality score threshold? Also, what other metrics should I take a look at? I'm working with metagenomics sequence data.

Answer 1

[ivivek_ngs]

Take a look at VCFTools. You can also take a look at both these threads 1 and 2 to understand how you can use. You can also use GATK but I have not tested non-gatk vcf with the -CombinVariants handle from GATK.

This is the current VCFTools link which is being maintaned

Alternatively take a look here

You can also take a look at this python code for filtering purpose

Too many options eh

Another tool that will serve the purpose is vcflib

Am sure all these will be able to help you out.