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=Haplotyping Project= [[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> name=Daniel:Notebook/Haplotyping format=%name/%year-%month-%day date=2014/02/01 view=oneyear </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.
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