Ylaine/2009-8-17
Jump to navigation
Jump to search
New 1K Genomes Reference
- BowtieMaq: Get 5 more matches and 5 fewer misses than when trio file used for comparison
- Should be more. Too many mismatches? Debugging code.
- Found bug: using reference instead of 1K call for comparison
../Scripts/hetOnly.pl no_dbSNP.new1K >no_dbSNP.new1K.het
- Quality and coverage alone are the best combination of parameters
- For n=50, p=0.3, f = 0.75:
' | Mean | Std |
FP | 25.26 | 7.32 |
MD | 15.20 | 6.17 |
Overall | 18.32 | 4.02 |
- Try with SOAP/SAM
../Scripts/compare1K.pl hiqual.no_dbSNP.het>hiqual.no_dbSNP.het.1K
- Place in separate folder
New Data
- SNPs thresholded on 8x coverage and 30x quality
Part 1
"What is the total size of exonic region that were covered by >=8x in this data set?"
WorkSpace/Exome/Solexa/NA12878/NA12878_061009_061109_080509_081309_40bp_sequence.bowtie.pileup
- Re-named 'orig.pileup'
genome-tech:Aug17Data ygerardin$ ../Scripts/threshold.pl orig.pileup 8 >cov8.temp& wc -l cov8.temp
- ANSWER: 23,830,845
Thoughts about classification
- We need a universal classification scheme that doesn't rely on knowing the classes of the training set.
- A more analogous problem is one of clustering