Hi SEQanswers 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 dependend.
Extracted Infos 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!
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 dependend.
Extracted Infos 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!