Daniel:Notebook/Haplotyping: Difference between revisions
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[[Daniel Jacobsen|Back to Notebook]] | [[Daniel Jacobsen|Back to Notebook]] | ||
[[Daniel:Experiments-Haplotyping|Experiment List]] | |||
==Aims== | |||
Overall aims for the paper, to be completed before publication | |||
*Compare BEAGLE computational inferences to experimental results | |||
*Create most complete diploid genome yet | |||
*Consensus results against published LFR data | |||
*Suggest the most cost effective way to phase a genome, including scale-up | |||
*Phase the HLA region with and without BEAGLE | |||
**Propose the most cost effective way to obtain this information on a per patient level | |||
===Specific Aims=== | |||
Table of current specific aims, to be completed within short time frames. Specific aims should make progress towards the completion of aims (above). | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
|align="center" width="500" | '''Specific Aim''' | |||
|align="center" width="65" | Date to Completion | |||
|align="center" width="65" | Date of Completion | |||
|align="center" width="250" | Notebook Link | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | Combine PGP1 data from Complete Genomics WGS to create more defendable/accurate VCF | |||
| align="center" | January 1, 2016 | |||
| align="center" | | |||
| align="center" | [[Daniel:Notebook/Haplotyping/MergeVCF|Merging Complete Genomics WGS data]] | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | Comparing data sets using consistent pairs method | |||
| align="center" | January 1, 2016 | |||
| align="center" | | |||
| align="center" | [[Daniel:Notebook/Haplotyping/ConsistentPairs|Consistent Pairs Method]] | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | Use BEAGLE to get inferences for PGP1 | |||
| align="center" | August 1, 2015 | |||
| align="center" | | |||
| align="center" | [[Daniel:Notebook/Haplotyping/BEAGLE|Using BEAGLE to infer population data]] | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | Assess variant calling using freebayes, create ROC | |||
| align="center" | January 1, 2016 | |||
| align="center" | | |||
| align="center" | [[Danie:Notebook/Haplotyping/Genotyping|Genotyping Samples]] | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left"| Combine Hi-C and BAC data to get more complete haplotypes | |||
| align="center" | August 1, 2015 | |||
| align="center" | | |||
| align="center" | [[Daniel:Notebook/Haplotyping/HiCBAC|Combining BAC and HiC Data]] | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | Use Eric's pipeline to segment SISSOR data | |||
| align="center" | January 1, 2015 | |||
| align="center" | | |||
| align="center" | [[Daniel:Notebook/Haplotyping/SISSORPipeline|SISSOR Segmentation Pipeline]] | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | Compare haplotypes in MHC Region | |||
| align="center" | January 1, 2015 | |||
| align="center" | | |||
| align="center" | | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" align="left" | CPT-Seq for PGP1 | |||
| align="center" | March 1, 2016 | |||
| align="center" | | |||
| align="center" | [[Daniel:Notebook/Haplotyping/CPTSeq-PGP1|CPT-Seq Pipeline]] | |||
|} | |||
==Data== | |||
List of pages related to data. | |||
*[[Daniel:Notebook/Haplotyping/DataMap|Data Map]] | |||
*[[Daniel:Notebook/Haplotyping/ReadCounts|Read Count Comparison]] | |||
*[[Daniel:Notebook/Haplotyping/Pipeline|Analysis Pipelines]] | |||
==Calendar and Experiments== | |||
==CPT-Seq for PGP1== | |||
[[Daniel:Notebook/Haplotyping/2016-1-31|High MW DNA Extraction]] | |||
<calendar> | <calendar> | ||
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view=oneyear | view=oneyear | ||
</calendar> | </calendar> | ||
==Data== | |||
[[Athurva Gore:LabNotes/ExomePipeline|Athurva's GATK Pipeline for Variant Calling]] | |||
This project utilizes several data sources. The data sources and relevant information are listed below. | |||
===BAC Data=== | |||
The BAC data is on genome miner, in the following path: | |||
*/media/LTS_33T/KZ_LTS33T/PGP1_BacPool | |||
The folder contains several subfolders: | |||
*old_calls | |||
**Contains the old variant call files | |||
*vcf_files | |||
**Contains a lot of vcf files | |||
*all_pools_combined | |||
**Contains all the heterozygous call files. Still unsure of the format | |||
*fixed.bam | |||
**Contains all of the bam files for each index | |||
*filtered_vcf | |||
**Seems to contain the newest .vcf files, probably the best ones to use | |||
*assembled_haplotypes | |||
**Contains the final phase output of HapCUT that was used for the BAC pools | |||
*het_sites | |||
**Contains the heterozygous site files for each chromosome. Still unsure of the format | |||
===HiC Data=== | |||
The HiC data is on TSCC, in the following path: | |||
*/oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c | |||
===Microfluidic Data=== | |||
The data sets are on genome miner, in the following paths: | |||
*'''Better one''':/media/Syn_15T/Eric_15T/PGP1_21 | |||
*'''Second best''':/media/Syn_15T/Eric_15T/PGP1_22 | |||
This data may have to be processed in the same manner as the BAC pools. If so, I will follow [[Athurva Gore:LabNotes/ExomePipeline|Athurva's pipeline]], which was used for the original BAC pool paper. |
Latest revision as of 21:52, 14 February 2016
Haplotyping Project[edit]
Aims[edit]
Overall aims for the paper, to be completed before publication
- Compare BEAGLE computational inferences to experimental results
- Create most complete diploid genome yet
- Consensus results against published LFR data
- Suggest the most cost effective way to phase a genome, including scale-up
- Phase the HLA region with and without BEAGLE
- Propose the most cost effective way to obtain this information on a per patient level
Specific Aims[edit]
Table of current specific aims, to be completed within short time frames. Specific aims should make progress towards the completion of aims (above).
Specific Aim | Date to Completion | Date of Completion | Notebook Link |
Combine PGP1 data from Complete Genomics WGS to create more defendable/accurate VCF | January 1, 2016 | Merging Complete Genomics WGS data | |
Comparing data sets using consistent pairs method | January 1, 2016 | Consistent Pairs Method | |
Use BEAGLE to get inferences for PGP1 | August 1, 2015 | Using BEAGLE to infer population data | |
Assess variant calling using freebayes, create ROC | January 1, 2016 | Genotyping Samples | |
Combine Hi-C and BAC data to get more complete haplotypes | August 1, 2015 | Combining BAC and HiC Data | |
Use Eric's pipeline to segment SISSOR data | January 1, 2015 | SISSOR Segmentation Pipeline | |
Compare haplotypes in MHC Region | January 1, 2015 | ||
CPT-Seq for PGP1 | March 1, 2016 | CPT-Seq Pipeline |
Data[edit]
List of pages related to data.
Calendar and Experiments[edit]
CPT-Seq for PGP1[edit]
<calendar> name=Daniel:Notebook/Haplotyping format=%name/%year-%month-%day date=2014/02/01 view=oneyear </calendar>
Data[edit]
Athurva's GATK Pipeline for Variant Calling
This project utilizes several data sources. The data sources and relevant information are listed below.
BAC Data[edit]
The BAC data is on genome miner, in the following path:
- /media/LTS_33T/KZ_LTS33T/PGP1_BacPool
The folder contains several subfolders:
- old_calls
- Contains the old variant call files
- vcf_files
- Contains a lot of vcf files
- all_pools_combined
- Contains all the heterozygous call files. Still unsure of the format
- fixed.bam
- Contains all of the bam files for each index
- filtered_vcf
- Seems to contain the newest .vcf files, probably the best ones to use
- assembled_haplotypes
- Contains the final phase output of HapCUT that was used for the BAC pools
- het_sites
- Contains the heterozygous site files for each chromosome. Still unsure of the format
HiC Data[edit]
The HiC data is on TSCC, in the following path:
- /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c
Microfluidic Data[edit]
The data sets are on genome miner, in the following paths:
- Better one:/media/Syn_15T/Eric_15T/PGP1_21
- Second best:/media/Syn_15T/Eric_15T/PGP1_22
This data may have to be processed in the same manner as the BAC pools. If so, I will follow Athurva's pipeline, which was used for the original BAC pool paper.