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.
•
written
by
StarCute
1 answer
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.
Log in to answer this question.
-
VCFfiltering
written by Peter •
-
Fixation index statistics in Case/Control study - thresholds
written by Lukas •
-
Recalculate R2 in imputed genotype data
written by coleman_jonathan
-
Validate the VCF file by freebayes
written by dorarinyo88 •
-
Filter SNPs on depth
written by Covux •
-
mpileup BAQ score
written by prasundutta87
-
Multi-sample variant calling
written by sumudu_rangika •
-
VCF merge and VCF intersect
written by Kousik •
-
Vcf Format And Filtering
written by Ashutosh Pandey
-
Variant Call Format - Explanation Of Quality Scores?
written by Ian
