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Concordance NGS and array genotypes

Hi Biostars folks,

For Sample based QC we would like to calculate the concordance of NGS genotypes from a VCF file and Illumina Array genotypes (HumanCoreExome-12 v1.0 ) from the FinalReport file.

The VCF file consist the genotypes 1/1 or 0/1 whereas the FinalReport file has the genotypes in form of the alleles strand dependent.

Extracted Info from the VCF file

chr    start    snp    ref    alt    GT
1    762273    rs3115849    G    A    0 /1
1    876499    rs4372192    A    G    1/ 1
1    877715    rs6605066    C    G    1/ 1
1    877831    rs6672356    T    C    1 /1
1    880238    rs3748592    A    G    1 /1

Extracted Infos from the FinalReport

chr    start    marker    allele A   allele B
1    152537954    exm-rs10888501      A    G
1    58915024      exm-rs10889092      G    G
1    63118196      exm-rs10889353      A    C
1    88112646      exm-rs10873862       A    C
1    76772328      exm-rs10873876       A    G
1    103133909    exm-rs10874639       A    G
1    93323971      exm-rs10874746       A    A

These are the infos I would use to estimate the concordance between the NGS and Array genotypes. Does someone have a clue how to approach this? Appreciate any help! Thx!

snp next-gen r sequencing
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updated by Ram Ram • written by genomixer • genomixer

what is the format of later file? First one is VCF , as I understand.

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written by cpad0112 cpad0112

its the FinalReport file which consist the raw data generated by the Illumina Genome Bead Studio.

and looks like this:

[Data]
SNP Name    Sample ID    Chr    Position    Allele1 - Top    Allele2 - Top    GC Score
rs2835478    DEWHH2342340297    21    38209770    A    A    0.7537
rs2835479    DEWHH2342340297    21    38210404    A    A    0.8255
rs283548      DEWHH2342340297    6    50966474    A    A    0.9138
rs2835482    DEWHH2342340297    21    38214047    A    G    0.9591
rs2835483    DEWHH2342340297    21    38216947    G    G    0.9252
rs2835511    DEWHH2342340297    21    38239499    A    G    0.7941

does this information help?

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updated by Ram Ram • written by genomixer • genomixer

1 answer

Thanks. See if Genotype Concordance Walker from GATK helps you
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written by cpad0112 cpad0112

it is meant to compare the results obtained from the same platform and is only suitable for compare VCFs. However I have read now that the array data could be exported with reference and alternate allele information which would make things easier.

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written by genomixer • genomixer

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