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, 02:18, 19 June 2014
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| <div class="mw-collapsible mw-collapsed" style="width:400px"> | | <div class="mw-collapsible mw-collapsed" style="width:400px"> |
− | View results | + | View the expected messages |
| <div class="mw-collapsible-content" style="width:800px"> | | <div class="mw-collapsible-content" style="width:800px"> |
| /home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz -r \ | | /home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz -r \ |
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| </div> | | </div> |
| </div> | | </div> |
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| + | After running annotation, you can check the annotation results. Let's look at the APOL g1 risk allele we manually examined in the SNP calling section. |
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| + | $GC/bin/tabix $OUT/assoc/snps.anno.vcf.gz 22:36661906 | head -1 | cut -f 1-8 |
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| + | <div class="mw-collapsible mw-collapsed" style="width:400px"> |
| + | View the annotation results |
| + | <div class="mw-collapsible-content" style="width:800px"> |
| + | 22 36661906 . A G 18 PASS DP=409;MQ=59;NS=62;AN=124;AC=2;AF=0.013827;AB=0.4065;AZ=-0.5287;FIC=-0.0092; |
| + | SLRT=-0.0075;HWEAF=0.0138;HWDAF=0.0276,0.0000;LBS=36,36,0,0,1,1,0,0;OBS=145,191,0,0,3,2,0,0;STR=-0.040; |
| + | STZ=-0.740;CBR=0.008;CBZ=0.144;IOR=0.000;IOZ=-1.370;AOI=-5.614;AOZ=-4.243;LQR=0.178;MQ0=0.000;MQ10=0.000;MQ20=0.000; |
| + | MQ30=0.000;SVM=1.51214;BAVGPOST=0.998;BRSQ=0.941;LDAF=0.0161;AVGPOST=1.0000;RSQ=1.0000;ERATE=0.0019;THETA=0.0013; |
| + | ANNO=Nonsynonymous:APOL1;ANNOFULL=APOL1/ENST00000397278.3:+:Nonsynonymous(AGC/Ser/S->GGC/Gly/G:Base1025/1197:Codon342/399:Exon6/6):Exon| |
| + | APOL1/ENST00000426053.1:+:Nonsynonymous(AGC/Ser/S->GGC/Gly/G:Base971/1143:Codon324/381:Exon5/5):Exon| |
| + | APOL1/ENST00000422706.1:+:Nonsynonymous(AGC/Ser/S->GGC/Gly/G:Base1025/1197:Codon342/399:Exon6/6):Exon| |
| + | APOL1/ENST00000319136.4:+:Nonsynonymous(AGC/Ser/S->GGC/Gly/G:Base1073/1245:Codon358/415:Exon7/7):Exon| |
| + | APOL1/ENST00000347595.7:+:Nonsynonymous(AGC/Ser/S->GGC/Gly/G:Base662/834:Codon221/278:Exon3/3):Exon| |
| + | APOL1/ENST00000397279.4:+:Nonsynonymous(AGC/Ser/S->GGC/Gly/G:Base1025/1197:Codon342/399:Exon6/7):Exon |
| + | </div> |
| + | </div> |
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| + | * What is the function of this variant? |
| + | * How many different transcript does the variant overlap with? |
| + | * How can you represent the variant in terms of amino acid changes? |
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| === Run Single Variant Analysis === | | === Run Single Variant Analysis === |