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. | ||
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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
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?