Ylaine/2009-8-17

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Revision as of 21:22, 17 August 2009 by >Ylaine (→‎Part 1)
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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