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

Revision as of 12:16, 15 December 2014

103 bytes added ,  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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exit PuTTY
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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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If you are interested in rare variants that are not identified by 1000G, you can extract them by running
 
If you are interested in rare variants that are not identified by 1000G, you can extract them by running
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  zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | grep -v "less"
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  zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | less
 
   
 
   
 
For example,  
 
For example,  
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* Q2. Looking at each functional category, which functional categories has largest fraction of SNPs failed filter? Why do you think it is?
 
* Q2. Looking at each functional category, which functional categories has largest fraction of SNPs failed filter? Why do you think it is?
 
* Q3. Can you exclude the sites that are also in dbSNP, and count how many nonsense variants are left?
 
* Q3. Can you exclude the sites that are also in dbSNP, and count how many nonsense variants are left?
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To also exclude those in dbsnp:
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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 "$1\t$F[6]" if ( /ANNO=([^;:]+)/)' | sort | uniq -c
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Exclude dbsnp and look at Stop_Gain variants
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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
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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/12388...12405"

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