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SeqShop: Variant Calling and Filtering for SNPs Practical, December 2014 (view source)

Revision as of 23:13, 23 November 2014

182 bytes removed ,  23:13, 23 November 2014
→‎Did I find interesting variants?
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Did you see a variant at the position?
 
Did you see a variant at the position?
   −
${GC}/bin/tabix ${OUT}/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 | head -1
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  22 36661906 . A G 23 PASS DP=409;MQ=59;NS=62;AN=124;AC=2;AF=0.013847;
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  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;
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AB=0.4169;AZ=-0.3525;FIC=-0.0089;SLRT=-0.0071;LBS=36,36,0,0,1,1,0,0;OBS=145,191,0,0,3,2,0,0;STR=-0.040;
−
                    FIC=-0.0092;SLRT=-0.0075;HWEAF=0.0138;HWDAF=0.0276,0.0000;LBS=36,36,0,0,1,1,0,0;
+
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;
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                    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;
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MQ10=0.000;MQ20=0.000;MQ30=0.000;SVM=1.45191 GT:DP:GQ:PL 0/0:4:28:0,12,65
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                    AOI=-5.614;AOZ=-4.243;LQR=0.178;MQ0=0.000;MQ10=0.000;MQ20=0.000;MQ30=0.000;SVM=1.51214
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              GT:DP:GQ:PL 0/0:4:28:0,12,65
      
Let's check the sequence data to confirm that the variant really exists
 
Let's check the sequence data to confirm that the variant really exists
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View Screenshot
 
View Screenshot
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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[[File:Samtoolstviewsnp.png|600px]]
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[[File:SamtoolstviewsnpNew.png|600px]]
 
</div>
 
</div>
 
</div>
 
</div>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12066"

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