HPG Variant - Bioinformatics and Genomics Department at CIPF

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IntroductionData generation pipelineNGSsequencerFastq fileQC, preprocessing and alignmentSAM / BAM fileQC, preprocessing and variant call analysisVCF fileQC and preprocessingVariant effect analysisGenomic-wide analysis
IntroductionVariant Call Format, VCFText file format (versions 4.0 and 4.1)Each line contains information about a positionof the genome##fileformat=VCFv4.0##INFO=##INFO=##INFO=##INFO=##reference=human_b36_both.fasta##FORMAT=##FORMAT=##FORMAT=#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA128781 52066 rs28402963 T C . PASS AA=C;DP=84 GT:GQ:DP 1/0:44:23 1/0:43:20 1/0:70:361 695745 . G A . PASS AA=.;DP=124 GT:GQ:DP 1|0:100:34 0|0:62:20 1|0:100:561 742429 rs3094315 G A . PASS AA=g;DP=132;HM2 GT:GQ:DP 1|1:100:38 1|1:59:30 1|1:100:441 742584 rs3131972 A G . PASS AA=a;DP=160;HM3 GT:GQ:DP 1|1:100:50 1|1:100:33 1|1:100:601 744366 rs3115859 G A . PASS AA=g;DP=127 GT:GQ:DP 1|1:80:31 1|1:100:34 1|1:100:451 746243 rs3131963 T A . PASS AA=t;DP=105 GT:GQ:DP 1|1:52:29 1|1:43:24 1|1:100:561 746775 rs6699990 A G . PASS AA=N;DP=120 GT:GQ:DP 0|1:100:34 0|0:89:30 0|0:100:461 747503 rs3115853 G A . PASS AA=-;DP=113 GT:GQ:DP 1|1:100:37 1|1:61:25 1|1:100:275
Page 7 and 8: HPC technologyOpenMPAPI for sharedm
Page 10: HPG VCF ToolsUtilities for VCF file
Page 14 and 15: HPG VCF ToolsHands-on demo stage 2!
Page 16 and 17: HPG VariantVariant Effect (I)A vari
Page 18 and 19: HPG VariantGWAS Analysis (I)Genomic
Page 20 and 21: HPG VariantGWAS Analysis (III)Comin
Page 22 and 23: HPG VariantHands-on demo final stag
Page 24: References1) A map of human genome

HPG Variant - Bioinformatics and Genomics Department at CIPF

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