Ylaine/2009-7-17
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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
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
- 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
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