Daniel:Notebook/Haplotyping
Haplotyping Project
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).
Aim | Date to Completion | Date of Completion | Link to posted data |
Concordance tables comparing SISSOR, BAC, and HiC data | January 1, 2015 | ||
Use BEAGLE to get inferences for PGP1 | January 1, 2015 |
Data
List of pages related to data.
Calendar
<calendar> name=Daniel:Notebook/Haplotyping format=%name/%year-%month-%day date=2014/02/01 view=oneyear </calendar>
Data
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's pipeline, which was used for the original BAC pool paper.