Question: Concordance Between Illumina 50 Snp Chip And Illumina Paired-End Ngs Snps
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gravatar for modi2020
5.1 years ago by
modi202030
United States
modi202030 wrote:

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

illumina ngs snps gatk • 1.6k views
ADD COMMENTlink modified 5.1 years ago by William4.4k • written 5.1 years ago by modi202030
0
gravatar for He
5.1 years ago by
He0
He0 wrote:

Thanks! That hot news!

ADD COMMENTlink written 5.1 years ago by He0
0
gravatar for William
5.1 years ago by
William4.4k
Europe
William4.4k wrote:

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.

ADD COMMENTlink written 5.1 years ago by William4.4k

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

ADD REPLYlink written 5.1 years ago by modi202030
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