Daniel:Notebook/Haplotyping: Difference between revisions

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The folder contains several subfolders:
The folder contains several subfolders:
#old_calls
*old_calls
##Contains the old variant call files
**Contains the old variant call files
#vcf_files
*vcf_files
##Contains a lot of vcf files
**Contains a lot of vcf files
#all_pools_combined
*all_pools_combined
##Contains all the heterozygous call files.  Still unsure of the format
**Contains all the heterozygous call files.  Still unsure of the format
#fixed.bam
*fixed.bam
##Contains all of the bam files for each index
**Contains all of the bam files for each index
#filtered_vcf
*filtered_vcf
##Seems to contain the newest .vcf files, probably the best ones to use
**Seems to contain the newest .vcf files, probably the best ones to use
#assembled_haplotypes
*assembled_haplotypes
##Contains the final phase output of HapCUT that was used for the BAC pools
**Contains the final phase output of HapCUT that was used for the BAC pools
#het_sites
*het_sites
##Contains the heterozygous site files for each chromosome. Still unsure of the format
**Contains the heterozygous site files for each chromosome. Still unsure of the format


===HiC Data===
===HiC Data===

Revision as of 01:13, 15 July 2014

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

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