Athurva Gore/LabNotes/2009-8-27: Difference between revisions

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** Reducing quality scores of end bases when SNPs found
** Reducing quality scores of end bases when SNPs found
** Reducing quality scores of all end bases
** Reducing quality scores of all end bases
==NA12878==
* Looked at HL006_s5 data
* Looked at HL006_s5 data
** Wanted to compare the small number of misses remaining to 1000 genome.
** Wanted to compare the small number of misses remaining to 1000 genome.
Line 23: Line 24:
  4      86        7
  4      86        7
* Lose only four hits, but eliminate most of the misses and all of the miscalls!
* Lose only four hits, but eliminate most of the misses and all of the miscalls!
* This makes sense, as with coverage < 4 (2 or 3 reads), we cannot be certain of the site.
** This makes sense, as with coverage < 4 (2 or 3 reads), we cannot be certain of the site.
==DF-6-9-9==
* Hoping to get a filter that allows good coverage but has ~5% of SNPs outside dbSNP only
* Can we accomplish this simply by thresholding coverage?

Revision as of 18:13, 27 August 2009

Navigation

To Do

  • Forms for Tech Transfer Office
  • Invoice for Zymo

Library-free Probesets

  • Investigate TDMR crash today; can we just skip that one site?

IPS and Cancer

  • Want to test various trimming methods to see which works best.
    • Removing end bases from reads with SNPs
    • Removing end bases from all reads
    • Reducing quality scores of end bases when SNPs found
    • Reducing quality scores of all end bases

NA12878

  • Looked at HL006_s5 data
    • Wanted to compare the small number of misses remaining to 1000 genome.
  • Found that if a coverage filter of >4 is set,
hits misses miscalls
Total Number		
29      111        7
Number with coverage < 4:		
4       86         7
  • Lose only four hits, but eliminate most of the misses and all of the miscalls!
    • This makes sense, as with coverage < 4 (2 or 3 reads), we cannot be certain of the site.

DF-6-9-9

  • Hoping to get a filter that allows good coverage but has ~5% of SNPs outside dbSNP only
  • Can we accomplish this simply by thresholding coverage?