Ylaine/2009-7-17

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Revision as of 21:20, 17 July 2009 by >Ylaine (→‎Maq/Sam)
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Bwa/Sam filtered variants

  • Re-do heatmap with consensus quality instead of SNP quality (see yesterday's entry)
bwaSam/NA12878_40bp_061109.sequence.pileup.variants.txt

File:Bwasam dbSNP q.jpg

Maq/Sam

  • Make heatmap from:
MaqSamTarget/snp.nonunique.dbSNP
  • Some SNPs in dbSNP have extremely high coverage, e.g. the highest coverage is at:
chr6    160384279               G       A/G     228     228     57      682     rs894817        A/G
    • Set heatmap upper bounds to go to next highest coverage value, 396

File:Maqsam nu dbSNP.jpg

  • Try using duplicate-filtered SNP set for fewer funny numbers
awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $8}' snp.chr.txt > snp.chr.qr.txt
../Scripts/matchCnsSnp2Ref_dbSNP.pl snp.chr.qr.txt > snp.chr.dbSNP.txt
  • False positives:
grep 'rs' snp.chr.dbSNP.txt > ../matchCnsSnp2Ref_AG.pl > snp.compare.in_dbSNP.txt
grep -v 'rs' snp.chr.dbSNP.txt >../matchCnsSnp2Ref_AG.pl > snp.nonunique.no_dbSNP.txt

File:Maqsam dbSNP.jpg

SNP Filtering

  • Look into reducing false positives (not in dbSNP, not found by 1000 genome)
    • Pattern classification: generate PDF in Matlab using 'ksdensity'
    • Matlab's optimization toolbox

Other

  • Summarize FP and FN rates for each method