Daniel:Notebook/Haplotyping: Difference between revisions
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The folder contains several subfolders: | 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=== | ===HiC Data=== |
Revision as of 01:13, 15 July 2014
Haplotyping Project
<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