Concordance Between Illumina 50 Snp Chip And Illumina Paired-End Ngs Snps

Question

[modi2020]

Hi everyone,

We have have genotype data (SNPs) on 50 K markers using Illumina SNP array. We now have fully sequenced these animals using NGS paired end sequencing and called SNPs on them using GATK. I was wondering if there was a tool or a way to see the concordance between the SNPs called using both programs since the GATK output is vcf format where as the genotypes using the array are in plink format. I know this could be tricky since some variants in GATK maybe called on the positive strand and some on the negative strand. However, I have looked for a solution online and there seems to be no straight way of doing this.

I would really appreciate any help with this.

Thank you

Answer 1

[He]

Thanks! That hot news!

Answer 2

[William]

What about GATK GenotypeConcordance:

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_GenotypeConcordance.html

Maybe you have to convert your SNP array call set to a simple vcf file.

[modi2020]

Thank you so much William. I will give that a try!