Ylaine/2009-7-17: Difference between revisions
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>Ylaine |
>Ylaine |
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(6 intermediate revisions by the same user not shown) | |||
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* Make heatmap from: | * Make heatmap from: | ||
MaqSamTarget/snp.nonunique.dbSNP | 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 | |||
[[Image: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: | |||
[[Image:Maqsam_dbSNP.jpg ]] | |||
grep 'rs' snp.chr.dbSNP.txt | ../Scripts/matchCnsSnp2Ref_AG.pl>snp.compare.in_dbSNP.txt | |||
grep -v 'rs' snp.chr.dbSNP.txt | ../Scripts/matchCnsSnp2Ref_AG.pl>snp.compare.no_dbSNP.txt | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''1K Genome''' | |||
| align="center" style="background:#f0f0f0;"|'''In dbSNP''' | |||
| align="center" style="background:#f0f0f0;"|'''Percent''' | |||
| align="center" style="background:#f0f0f0;"|'''Not in dbSNP''' | |||
| align="center" style="background:#f0f0f0;"|'''Percent''' | |||
|- | |||
| Match||7886||76.73%||216||1.69% | |||
|- | |||
| Miss||1137||11.06%||12506||97.66% | |||
|- | |||
| Mismatch||1255||12.21%||83||0.65% | |||
|- | |||
| Total||10277||||12805|| | |||
|- | |||
| | |||
|} | |||
* FP rate: '''48.04%''' | |||
[[Image:Maqsam_nodbSNP_rmdup.jpg ]] | |||
==SNP Filtering== | ==SNP Filtering== | ||
Line 14: | Line 44: | ||
==Other== | ==Other== | ||
* | * Summarize FP and FN rates for each method |
Latest revision as of 22:09, 17 July 2009
Bwa/Sam filtered variants[edit]
- Re-do heatmap with consensus quality instead of SNP quality (see yesterday's entry)
bwaSam/NA12878_40bp_061109.sequence.pileup.variants.txt
Maq/Sam[edit]
- 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 | ../Scripts/matchCnsSnp2Ref_AG.pl>snp.compare.in_dbSNP.txt grep -v 'rs' snp.chr.dbSNP.txt | ../Scripts/matchCnsSnp2Ref_AG.pl>snp.compare.no_dbSNP.txt
1K Genome | In dbSNP | Percent | Not in dbSNP | Percent |
Match | 7886 | 76.73% | 216 | 1.69% |
Miss | 1137 | 11.06% | 12506 | 97.66% |
Mismatch | 1255 | 12.21% | 83 | 0.65% |
Total | 10277 | 12805 | ||
- FP rate: 48.04%
SNP Filtering[edit]
- 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[edit]
- Summarize FP and FN rates for each method