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== Compare Common SNV in Chamber 15/18 and Complete Genomics Data (by Position Only) == $ awk -F"\t" 'FILENAME=="PGP1_21_ch15.unique.haplotype2.HLA0.vcf"{A[$1$2$4]=$1$2$4} FILENAME=="PGP1_21_ch18.unique.haplotype2.HLA0.vcf"{if(A[$1$2$4]){print}}' PGP1_21_ch15.unique.haplotype2.HLA0.vcf PGP1_21_ch18.unique.haplotype2.HLA0.vcf > PGP1_21_ch15ch18.unique.HLA0.commonpos.vcf $ wc -l PGP1_21_ch15ch18.unique.HLA0.commonpos.vcf 1310 PGP1_21_ch15ch18.unique.HLA0.commonpos.vcf $ awk -F"\t" 'FILENAME=="PGP1_21_ch15.unique.haplotype2.HLA0.vcf"{A[$1$2$4]=$1$2$4} FILENAME=="pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf"{if(A[$1$2$4]){print}}' PGP1_21_ch15.unique.haplotype2.HLA0.vcf pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf > PGP1_21_ch15CompleteGenomics.unique.HLA0.commonpos.vcf & $ wc -l PGP1_21_ch15CompleteGenomics.unique.HLA0.commonpos.vcf 1651 PGP1_21_ch15CompleteGenomics.unique.HLA0.commonpos.vcf $ awk -F"\t" 'FILENAME=="PGP1_21_ch18.unique.haplotype2.HLA0.vcf"{A[$1$2$4]=$1$2$4} FILENAME=="pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf"{if(A[$1$2$4]){print}}' PGP1_21_ch18.unique.haplotype2.HLA0.vcf pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf > PGP1_21_ch18CompleteGenomics.unique.HLA0.commonpos.vcf & $ wc -l PGP1_21_ch18CompleteGenomics.unique.HLA0.commonpos.vcf 1435 PGP1_21_ch18CompleteGenomics.unique.HLA0.commonpos.vcf $ awk -F"\t" 'FILENAME=="PGP1_21_ch15CompleteGenomics.unique.HLA0.commonpos.vcf"{A[$1$2$4]=$1$2$4} FILENAME=="PGP1_21_ch18CompleteGenomics.unique.HLA0.commonpos.vcf"{if(A[$1$2$4]){print}}' PGP1_21_ch15CompleteGenomics.unique.HLA0.commonpos.vcf PGP1_21_ch18CompleteGenomics.unique.HLA0.commonpos.vcf > PGP1_21_ch15ch18CompleteGenomics.unique.HLA0.commonpos.vcf & $ wc -l PGP1_21_ch15ch18CompleteGenomics.unique.HLA0.commonpos.vcf 1097 PGP1_21_ch15ch18CompleteGenomics.unique.HLA0.commonpos.vcf * Number of False Positives = Difference of SNV Calling by just position and actual SNV Calling * [[File:VennDiagramHLAP2&CompleteGenomicsbyPosition.jpg|300px]]
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