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SeqShop: Calling Your Own Genome, May 2015 (view source)

Revision as of 12:10, 22 May 2015

290 bytes added ,  12:10, 22 May 2015
→‎Annotation / Lookup against dbSNP
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== Thursday ==
 
== Thursday ==
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== Friday ==
 
== Friday ==
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[[SeqShop: Ancestry On Your Own Genome, May 2015]]
 
[[SeqShop: Ancestry On Your Own Genome, May 2015]]
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=== Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
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=== Setup Variables ===
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Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]]
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Set these values.  Also, be sure to specify your sample name instead of SampleXX
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export SAMPLE=SampleXX
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or
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export SAMPLE=NA12878
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Point to your GotCloud & your output directory:
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export GC=~/seqshop/gotcloud
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export OUT=~/$SAMPLE/output
    
=== Reviewing Indel Results ===
 
=== Reviewing Indel Results ===
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Set these values.  Also, be sure to specify your sample name (or NA12878) instead of SampleXX
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export SAMPLE=SampleXX
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source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
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Look in the output directory
 
Look in the output directory
 
  ls ~/$SAMPLE/output
 
  ls ~/$SAMPLE/output
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The insertion deletion ratio increases from 0.91 to 0.92.   
 
The insertion deletion ratio increases from 0.91 to 0.92.   
    +
=== Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
 +
Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]]
    
=== Friday: Reviewing SNPCALL Results ===
 
=== Friday: Reviewing SNPCALL Results ===
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=== Friday : More SNP Analysis ===
 
=== Friday : More SNP Analysis ===
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In addition, set another environmental variable for locating the binaries for custom analysis
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==== Environmental Variables ====
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export HK=/net/seqshop-server/home/hmkang/apigenome/bin
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  export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/
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If you didn't set the environmental variable, you can set it again
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  export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref
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export GC=~/seqshop/gotcloud
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  source /net/seqshop-server/home/mktrost/seqshop/setup.txt
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  export SAMPLE=SampleXX (MAKE SURE TO CHANGE XX to your number or use NA12878 instead)
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source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
     −
In addition, set another environmental variable for locating the binaries for custom analysis
     −
  export HK=/home/hmkang/apigenome/bin/
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  export SAMPLE=SampleXX
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export OUT=~/$SAMPLE/output
    
==== Annotation / Lookup against dbSNP ====
 
==== Annotation / Lookup against dbSNP ====
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If you want to add rsIDs to your variant files, you can do this by running the following command
 
If you want to add rsIDs to your variant files, you can do this by running the following command
   −
  $HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz
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  $HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbsnp_142.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz
 
   
 
   
 
If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs
 
If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs
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  $HK/run-command-wgs --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6
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  $HK/run-make --repeat-chr --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbsnp_142.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6 --out runmake.rsid
   −
Looking up SNPs by rsID is possible by (for example)
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Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position?
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  $HK/vcf-lookup-rsid --vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --sepchr --rs rs17766217
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  $HK/tabix $OUT/vcfs/chr8/chr8.filtered.rsid.vcf.gz 8:128504497 | less
 
* Be sure to look at the QUAL & your sample's PL, and not just the GL field.  Check if QUAL is 0 or PL is 0,0,0 - NS is also probably 0; DP is probably 0.  That means you probably didn't have any copies, so your GT may not be correct/is unknown.
 
* Be sure to look at the QUAL & your sample's PL, and not just the GL field.  Check if QUAL is 0 or PL is 0,0,0 - NS is also probably 0; DP is probably 0.  That means you probably didn't have any copies, so your GT may not be correct/is unknown.
    
If you want to browse the rsIDs of known GWAS SNPs, you can do this by
 
If you want to browse the rsIDs of known GWAS SNPs, you can do this by
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  cut -f 1,8,22 $HK/../data/gwascatalog/gwascatalog.txt | less
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  cut -f 1,8,12,13,22 $HK/../data/gwascatalog/gwascatalog.txt | grep -w rs17766217
    
==== Annotating your genome ====
 
==== Annotating your genome ====
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Or you can run multiple chromosomes in parallel in one command
 
Or you can run multiple chromosomes in parallel in one command
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  $HK/run-command-wgs --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --numjobs 6  
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  $HK/run-make --repeat-chr --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --numjobs 6 --out runmake.anno
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+
 
 
==== Extracting only exonic SNPs ====
 
==== Extracting only exonic SNPs ====
    
If you want to look at the exonic SNPs, you can extract using the following command
 
If you want to look at the exonic SNPs, you can extract using the following command
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  $HK/run-command-wgs --cmd "($HK/tabix -H $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz; zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz | grep Exon;)| $HK/bgzip -c > $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz" --numjobs 6
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  $HK/run-make --repeat-chr --cmd "($HK/tabix -H $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz; zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz | grep Exon;)| $HK/bgzip -c > $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz" --numjobs 6 --out runmake.exome
    
And they can be combined as follows
 
And they can be combined as follows
 
  (zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz; zcat $OUT/vcfs/chr[2-9]/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chr??/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chrX/chrX.filtered.rsid.anno.exon.vcf.gz | grep -v ^#) | $HK/bgzip -c > $OUT/wgs.filtered.rsid.anno.exon.vcf.gz
 
  (zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz; zcat $OUT/vcfs/chr[2-9]/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chr??/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chrX/chrX.filtered.rsid.anno.exon.vcf.gz | grep -v ^#) | $HK/bgzip -c > $OUT/wgs.filtered.rsid.anno.exon.vcf.gz
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$HK/tabix -pvcf $OUT/wgs.filtered.rsid.anno.exon.vcf.gz
    
==== Exonic Variants NOT found by 1000G ====
 
==== Exonic Variants NOT found by 1000G ====
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Want to see this from the BAM file?  Use samtools tview:
 
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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  $GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $REF/hs37d5.fa
 
Use 'g' & enter the Chr:Pos
 
Use 'g' & enter the Chr:Pos
 
* Some patterns may indicate not real variants.
 
* Some patterns may indicate not real variants.
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The phred score at the last column quantifies the degree of functional significance
 
The phred score at the last column quantifies the degree of functional significance
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== OVERALL COURSE FEEDBACK! ==
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Please provide feedback:
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https://docs.google.com/forms/d/1pxfPXKwWfA71ZJM99Sevs3MwAUz2UbHAR8dnRI-kRNM/viewform
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13415...13448"

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