Daniel:Notebook/Haplotyping

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Revision as of 23:34, 7 December 2015 by >Djacobse (→‎Specific Aims)
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Haplotyping Project

Back to Notebook

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).

Specific Aim Date to Completion Date of Completion Notebook Link
Comparing data sets using consistent pairs method January 1, 2016
Use BEAGLE to get inferences for PGP1 August 1, 2015
Assess variant calling using freebayes, create ROC January 1, 2016
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

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.