Athurva Gore/LabNotes/2009-8-20: Difference between revisions

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>Ajgore
(New page: {{ AGLabEntry|2009-8-19|2009-8-21 }} =False Positive SNPs= * Currently checking to see if clonal reads could be influencing false positive SNPs. * Added a step to variant caller that remo...)
 
>Ajgore
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* Added a step to variant caller that removes clonal reads (rmdup)
* Added a step to variant caller that removes clonal reads (rmdup)
* Testing on HL003_merged "high false positive" set.
* Testing on HL003_merged "high false positive" set.
** Removing clonal reads does not have any effect; downsampling seems to remove them in a similar way
** No advantage gained.
* MAQ, however, does something more interesting
** MAQ only calls 2500 SNPs from HL003 NA12878 set.
** Most of them are at dbSNP locations (only 300 not)
** MAQ is being much more conservative somehow
*** Taking into account mapping quality?  What about taking into account neighboring consensus quality?

Revision as of 22:08, 20 August 2009

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False Positive SNPs

  • Currently checking to see if clonal reads could be influencing false positive SNPs.
  • Added a step to variant caller that removes clonal reads (rmdup)
  • Testing on HL003_merged "high false positive" set.
    • Removing clonal reads does not have any effect; downsampling seems to remove them in a similar way
    • No advantage gained.
  • MAQ, however, does something more interesting
    • MAQ only calls 2500 SNPs from HL003 NA12878 set.
    • Most of them are at dbSNP locations (only 300 not)
    • MAQ is being much more conservative somehow
      • Taking into account mapping quality? What about taking into account neighboring consensus quality?