Ylaine/2009-8-26

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Clustering[edit]

  • Re-ran clustering with similar results. Only difference is 1 false SNP that was accepted in the first round instead of the second round.

File:Aug17 nodbSNP.jpg File:Aug17 cluster1.jpg File:Aug17 cluster2.jpg

  • Commands:
[error, groups] = snpCluster(match,miss);
    • 328 accepted, 3102 rejected, total error rate of 8.45% (46.46% MD, 1.42% FP)
    • 287 true and 41 false
groups_match = groups(1:536);
rejects_match = match(find(groups_match==2),:);
groups_miss = groups(537:3430);
rejects_miss = miss(find(groups_miss==2),:);

[error, groups2] = snpCluster(rejects_match, rejects_miss);
    • 214 accepted, 2888 rejected, total error rate of 6.61% (48.19% MD, 2.98% FP)
    • 129 true and 85 false

Testing Filter[edit]

  • Validate method on another test set:
/Users/ajgore/YlaineReads/s_5_sequence.bowtie.sam.variants.txt
grep -v 'rs' orig.snp > nodbsnp
../Scripts/compare1K.pl nodbsnp > 1k
  • Remove extraneous information:
grep -v '#' 1k>1kcompare
  • Partition based on matching (lump mismatches with misses
grep '   match' 1kcompare > nodbsnp.match
grep -v '        match' 1Kkcompare > nodbsnp.miss
    • Out of 21322, only 66 match 1000 Genomes: clustering will probably not be useful

False Negatives[edit]

cat gold.covereda*>gold.covered
../Scripts/matchGold.pl gold.covered>gold.match
    • 9553 total: 7869 match, 1182 miss, 512 mismatch
../Scripts/threshold.pl gold.match 2 > gold.match2
' Correct SNP ' Incorrect ' Missed ' Total
1x 7859 82.27% 512 5.36% 1182 12.37% 9553
2x 7715 85.97% 348 3.88% 911 10.15% 8974
8x 6732 94.05% 57 0.80% 369 5.16% 7158
20x 4997 96.37% 10 0.19% 178 3.43% 5185

File:Aug17 fn.bmp

Poster[edit]

  • Determine whom to acknowledge for experimental results