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SeqShop: Calling Your Own Genome, December 2014 (view source)

Revision as of 12:16, 15 December 2014

307 bytes removed ,  12:16, 15 December 2014
→‎Wednesday FEEDBACK!
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=== Tuesday FEEDBACK! ===
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Please provide feedback on the lectures/tutorials from today:
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https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform
   
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== Wednesday ==
 
== Wednesday ==
 
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==== Wednesday FEEDBACK! ====
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Please provide feedback on the lectures/tutorials from today:
  −
  −
https://docs.google.com/a/umich.edu/forms/d/1CCHL9ODPsw4jX4hj0kGo6AMHwT4Gam0IpKNRnIR9yMk/viewform
      
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== Thursday ==
 
== Thursday ==
 
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  zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" |grep -v rs | perl -lane 'print "$_" if ( /ANNO=Stop_Gain/)' |grep -w PASS
 
  zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" |grep -v rs | perl -lane 'print "$_" if ( /ANNO=Stop_Gain/)' |grep -w PASS
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Want to see this from the BAM file?  Use samtools tview:
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$GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $GC/gotcloud.ref/human.g1k.v37.fa
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Use 'g' & enter the Chr:Pos
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* Some patterns may indicate not real variants.
    
If you want to know predicted functional significance of a particular variant, you can search by
 
If you want to know predicted functional significance of a particular variant, you can search by
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===== WORKSHOP FEEDBACK! =====
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Please provide feedback on the workshop in general:
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https://docs.google.com/forms/d/1f8HjTKvxgYuApl9dLNqbW9Su3N3v9jtMpEDcbPJ1PYk/viewform
   
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12392...12405"

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