Athurva Gore/LabNotes/2009-8-17: Difference between revisions
Jump to navigation
Jump to search
>Ajgore (New page: {{ AGLabEntry|2009-8-14|2009-8-18 }} =Probe Generation= * '''DONE''' ** KKESH72 ** RPLCACRD ** CpG-SNP set (with 80 bp gap) ** FlyDup936 ** A-to-I Probes for Erez and Billy * '''CURRENTLY...) |
>Ajgore |
||
(6 intermediate revisions by the same user not shown) | |||
Line 8: | Line 8: | ||
** FlyDup936 | ** FlyDup936 | ||
** A-to-I Probes for Erez and Billy | ** A-to-I Probes for Erez and Billy | ||
** LeeCancer (on opposite strand to target cDNA) | |||
** LeeXGenes (on opposite strand to target cDNA) | |||
** ZhangSNP (on opposite strand to target cDNA) | |||
* '''CURRENTLY RUNNING:''' | * '''CURRENTLY RUNNING:''' | ||
** FlyDup901 | ** FlyDup901 | ||
** FlyDup5279 | ** FlyDup5279 | ||
* '''TO RERUN:''' | * '''TO RERUN:''' | ||
** TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?) | ** TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?) | ||
=Exome Sequencing Project= | |||
* Text of Dr. Zhang's Email: | |||
I’m sending you a list of NA12878 variants called from ~40 millions high quality reads. I have pretty good | |||
feeling about these calls using a simple filter of depth >=8x and SNP quality >=30. Can you please help me to | |||
get the following numbers: | |||
(1) What is the total size of exonic region that were covered by >=8x in this data set? For that you will | |||
need the pileup file which is available on genome-tech in my folder: WorkSpace/Exome/Solexa/NA12878/ | |||
NA12878_061009_061109_080509_081309_40bp_sequence.bowtie.pileup | |||
(2) How many variants found are within these regions and how many located outside of our target regions | |||
(non-specific capture)? | |||
(3) How many SNPs and variants did you see in Hapmap and 1KG data sets, and how consistent our variant | |||
calls are compared with the reference data? | |||
(4) If you remove some apparent false-positives that tends to localize very close to each other (probably | |||
due to mapping issues), what the numbers are in (3)? | |||
(5) Using 1KG data as reference, what is our false positive rate as the function of the filter we used? | |||
This could be plotted as a curve. Also what is the total variants we can call as the function of false- | |||
positive rate? | |||
We will submit this data set to the exome sequencing program to compare with data generated by two other | |||
centers. Ideally we should have these numbers before we submit the data. | |||
Thanks! | |||
Kun | |||
* Ylaine is currently working on #1 | |||
* I am working on number 4 - building null distribution for 1KG set to determine distance between two adjacent SNPs. | |||
=SNP Distribution Filtering= | |||
* Many of our false positives appear to be close to each other. | |||
** Can we build a distribution of the distance between true SNPs? | |||
** What about if we neglect SNPs in dbSNP; can this be used to aid filtering? | |||
* Downloaded NA12878 1KG SNP call file from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20080812_ceu_trio/NA12878/NA12878.snp.flt | |||
** File contains a list of called SNPs. | |||
*'''CURRENTLY: Running script to extract list of 1KG SNPs inside probe range''' | |||
=IPS and Cancer= | |||
* Need to be certain of SNPs used. | |||
* Can check other data sets (HL_003, HL_004, HL_008?) |
Latest revision as of 23:17, 17 August 2009
[edit]
Probe Generation[edit]
- DONE
- KKESH72
- RPLCACRD
- CpG-SNP set (with 80 bp gap)
- FlyDup936
- A-to-I Probes for Erez and Billy
- LeeCancer (on opposite strand to target cDNA)
- LeeXGenes (on opposite strand to target cDNA)
- ZhangSNP (on opposite strand to target cDNA)
- CURRENTLY RUNNING:
- FlyDup901
- FlyDup5279
- TO RERUN:
- TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?)
Exome Sequencing Project[edit]
- Text of Dr. Zhang's Email:
I’m sending you a list of NA12878 variants called from ~40 millions high quality reads. I have pretty good feeling about these calls using a simple filter of depth >=8x and SNP quality >=30. Can you please help me to get the following numbers: (1) What is the total size of exonic region that were covered by >=8x in this data set? For that you will need the pileup file which is available on genome-tech in my folder: WorkSpace/Exome/Solexa/NA12878/ NA12878_061009_061109_080509_081309_40bp_sequence.bowtie.pileup (2) How many variants found are within these regions and how many located outside of our target regions (non-specific capture)? (3) How many SNPs and variants did you see in Hapmap and 1KG data sets, and how consistent our variant calls are compared with the reference data? (4) If you remove some apparent false-positives that tends to localize very close to each other (probably due to mapping issues), what the numbers are in (3)? (5) Using 1KG data as reference, what is our false positive rate as the function of the filter we used? This could be plotted as a curve. Also what is the total variants we can call as the function of false- positive rate? We will submit this data set to the exome sequencing program to compare with data generated by two other centers. Ideally we should have these numbers before we submit the data. Thanks! Kun
- Ylaine is currently working on #1
- I am working on number 4 - building null distribution for 1KG set to determine distance between two adjacent SNPs.
SNP Distribution Filtering[edit]
- Many of our false positives appear to be close to each other.
- Can we build a distribution of the distance between true SNPs?
- What about if we neglect SNPs in dbSNP; can this be used to aid filtering?
- Downloaded NA12878 1KG SNP call file from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20080812_ceu_trio/NA12878/NA12878.snp.flt
- File contains a list of called SNPs.
- CURRENTLY: Running script to extract list of 1KG SNPs inside probe range
IPS and Cancer[edit]
- Need to be certain of SNPs used.
- Can check other data sets (HL_003, HL_004, HL_008?)