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, 12:16, 15 December 2014
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| exit PuTTY | | exit PuTTY |
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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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| </div> | | </div> |
| </div> | | </div> |
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| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
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| == Wednesday == | | == Wednesday == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| exit PuTTY | | exit PuTTY |
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− | ==== Wednesday FEEDBACK! ====
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− | Please provide feedback on the lectures/tutorials from today:
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− |
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− | https://docs.google.com/a/umich.edu/forms/d/1CCHL9ODPsw4jX4hj0kGo6AMHwT4Gam0IpKNRnIR9yMk/viewform
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| </div> | | </div> |
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| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
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| == Thursday == | | == Thursday == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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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: |
| + | 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 |
| + | 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: |
| + | $GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $GC/gotcloud.ref/human.g1k.v37.fa |
| + | Use 'g' & enter the Chr:Pos |
| + | * Some patterns may indicate not real variants. |
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| 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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| </div> | | </div> |
| </div> | | </div> |