I am using Mpileup using SAM tools version 1.2+htslib-1.2.1 to generate variants. The tool works fine and gives me an output in VCF version 4.2. However there is no such description of VCF fromat file as in other VCF version 4.1. So it is hard to understand the file.Still I go convert vcf to tab delimit my file and I can see samples with all the details
etc. But When I apply filter on VCF file for quality or REF not equal to ALT allele, the number of lines comes to half of original file, but when I tab limit this vcf file I can see nothing except the first line with information. I dont understand whats going on. How to apply filter is my question so that I can only get SNPs from a list of variants ??
I have tried using the same dataset with FREE BAYES and it runs well.
I have seen something very peculiar in freebayes also. When I filter my vcf file with one aspect I get an output and when using this as an input for a second step I get reults but on tab delimiting I see all information columns merged together.Is there some thing wrong with VCF tool manipulation to convert to tab delimit. Or is there anythiny I am doing wrong?
Any help will be appreciated.