Genotype Data And Exome Sequencing Data Sensitivity

Question

[Liyf]

I genotyped a sample by Illumina SNP array and I sequenced its exome sequencing data. What is the sensitivity of genotype calling from sequencing data? Is there already perl script?

[user56]

So which one is more accurate - genotyping or sequencing?

Answer 1

[Sean Davis]

You might want to look at these two tools:

http://vcftools.sourceforge.net/perl_module.html#vcf-compare

http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval

[Liyf]

Many thanks. I will have a try.

[Liyf]

But I do not found how to download VariantEval, I think it will be fit for me.

[Sean Davis]

VariantEval is part of GATK. You will need to download the GATK software.