quality check of vcf files

Question

[rthapa]

Hi,

I have a multiple vcf files for the same sample. I want to select the best single vcf file from all. I don't know the sequencing depth of the samples. I wonder if there is a way to select the best one based on the quality scores of SNP calls from the vcf files.

Thanks

Answer 1

[a.alnawfal.1992]

Hi, there are a lots of tools give you sammuray about you VCF file, like:

vt

vt peek

GATK

gatk VariantEval

rtg-tools

rtg vcfstats

BCF-Tools

bcftools stats

and a lot more tools do the same, as i do not know what is you experiments and you goal (what you want to do exactly) the list of above tools is the best answer. but remember there are a lot of parameter (in addition to QUAL) represent overall quality of VCF like DP, MQ ..ect., even looking inside BAM file (RAW ALIGNMENT) is very importent to assess the variant quality. if you have a Baseline VCF file forget all above tools and proceed with:

rtg vcfeval

i hope it helps