Daniel:Notebook/Haplotyping

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Revision as of 17:51, 22 August 2014 by >Djacobse
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Haplotyping Project

Back to Notebook

Experiment List

<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.