Ylaine/2009-8-25
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Improving Clustering[edit]
- Re-cluster rejects from first round
[error, groups] = snpCluster(nodb_match,[nodb_mismatch; nodb_miss]); [reject_match, reject_miss] = filterSNPs(nodb_match, [nodb_mismatch; nodb_miss], groups); [error, groups2] = snpCluster(reject_match(:,1:3), reject_miss(:,1:3));
- Best combination so far is quality, coverage, and 10*heterozygosity, with 6.7% error: 49% MD, 3.01% FP
- Rejects 2890 SNPs
- Minimize over weights on heterozygosity: local minimum around 14, becomes erratic about 14.5. Lowest error rate is 6.64% (rejects 2888 SNPs)
' | No dbSNP | Clustering |
Match 1k | 536 | 416 |
Miss 1k | 2821 | 86 |
Mismatch 1k | 73 | 40 |
SNPs Called | 20761 | 17873 |
False Call rate | 0.139395983 | 0.00704974 |
- 20x decrease in error
- These are similar to last week's but now an accurate call is defined as being in dbSNP OR matching 1K Genomes
File:Aug17 percent acc.jpg File:Aug17 percent acc closeup.jpg
False Negatives[edit]
- Same procedure as on 7/30
../Scripts/snpCovered2.pl gold.xaa orig.pileup > gold.coveredaa&