Daniel:Notebook/Haplotyping/DataMap: Difference between revisions

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===Processing Reference Data===
===Processing Reference Data===


The reference data was processed in several steps.
The reference data information can be found [[Daniel:Notebook/Haplotyping/MergeVCF|here]]
 
#Read in reference data and merge using 2/3 voting method (If site was called heterozygous in 2/3 cell lines)
##[[File:Vcfmergingfiles.mcode.completegenomics.zip‎|M code]]
#Convert the data to hg19 to be consistent with the other data


===Data Update Dec. 2015===
===Data Update Dec. 2015===
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|- style="font-size:12pt"  valign="bottom"
|- style="font-size:12pt"  valign="bottom"
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1920656431 BEAGLE Data Map]
| [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1920656431 BEAGLE Data Map]
|  
| [[Daniel:Notebook/Haplotyping/BEAGLE|BEAGLE Data Processing]]


|}
|}

Latest revision as of 18:11, 15 December 2015

Data Map[edit]

Back to Notebook

This page contains the data map for the haplotyping project, specifically tables that outline locations of each of the data types.

Reference Data[edit]

The reference data is the data used to create the "true" VCFs, since HAPCUT requires a true vcf file as input which informs it where the relevant sites are. The original PGP1 data is in genome miner in the directory /home/kunzhang/genomeSeq/Data/PGP1_CGI_WGS. The data was from 3 different cell lines.

Processing Reference Data[edit]

The reference data information can be found here

Data Update Dec. 2015[edit]

It occurs to me this needs to be better updated, so I'm linking to a google doc.

Data Map Notebook Link
Hi-C Data Map
BAC Data Map Processing BAC Data
LFR Data Map Processing LFR Data
BAC+Hi-C Data Map BAC and Hi-C Data Processing
LFR + Hi-C Data Map LFR and Hi-C Data Processing
BAC+Hi-C+LFR Data Map LFR+BAC+Hi-C Data Processing
BEAGLE Data Map BEAGLE Data Processing

Hi-C Data[edit]

File Type System Path File(s)
VCF TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/snps/ pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3.vcf
VCF-by chromosome TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/snps/ chr*/sorted.chr*.pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3_clean_final.vcf
bam files-original TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c PGP1.Rep1.rg.nodup.final_PE_sort.bam
bam files-by chrom TSCC /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c chr*/PGP1.final.chr*.corrected.bam
HAIRS-raw TSCC /oasis/tscc/scratch/djacobse/haplotypeSeqData/HAIRS fragments.chr*.hic.txt
HAIRS-merge XXXX XXXX XXXX
haplotypes TSCC /oasis/tscc/scratch/djacobse/haplotypeSeqData/hapcut_results haplotype.chr*.hic.txt

Notes:

  • * chromosomes 1 to 22

Bacterial Artificial Chromosome (BAC) Data[edit]

File Type System Path File(s)
VCF-All Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/filtered_vcf pgp1_variants_bac_all.Indx73to96.vcf
VCF-by chromosome XXXX XXXX XXXX
bam files-original Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/fixed.bam PGP1_***BacPool_Indx**.fixed.bam
bam files-contigs Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bacContigs Indx**.bacs.bam
bam files-by chrom Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/bams_by_chromosome chr*/chr*.Indx**.bam
HAIRS-raw Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/HAIRS chr*/chr*.Indx**.bam
HAIRS-merge Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/HAIRS chr*/fragments.chr*.bac.txt
haplotypes Genome Miner /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/haplotypes haplotype.chr*.bac.txt

Notes:

  • * chromosomes 1 to 22
  • ** indexes 73 to 96
  • *** 3 or 6, some 6 pools (85 and 92) also have a **.2.fixed.bam notation

SISSOR DATA[edit]

PGP1-21[edit]

File Type-PGP1_21 Path File(s)
VCF-by chrom /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber chamber**/chamber**_pgp1_21.snps.raw.vcf
VCF-pgp1_21 /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber pgp1.22.SISSOR.vcf
bam files-original /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/data_by_chamber chamber**_pgp1_21.BQSR.realigned.bam
bam files-contigs /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs chamber**.contigs.bam
bam files-by chrom /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/bams_by_chromosome chr*/chr*.chamber**.bam
HAIRS-raw /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS chr*/fragments.chr*.chamber**.txt
HAIRS-merge /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/HAIRS chr*/fragments.chr*.pgp1_21.txt
haplotypes /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/haplotypes haplotype.chr*.sissor.txt

Notes:

  • * chromosomes 1 to 22
  • ** chambers 1 to 24

PGP1-22[edit]

File Type-PGP1_22 Path File(s)
VCF-by chrom /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber chamber**/pgp22_chamber**.snps.raw.vcf
VCF-pgp1_22 /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber pgp1.22.SISSOR.vcf
bam files-original /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber chamber**/pgp22_chamber*.BQSR.realigned.bam
bam files-contigs /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp21/contigs chamber**.contigs.bam
bam files-by chrom /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/bams_by_chromosome chr*/chr*.chamber*.bam
HAIRS-raw /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/HAIRS chr*/fragments.chr*.chamber*.txt
HAIRS-merge /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/HAIRS chr*/fragments.chr*.pgp1_21.txt
haplotypes /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/haplotypes haplotype.chr*.sissor.txt

Notes:

  • * chromosomes 1 to 22
  • ** chambers 1 to 24

Merge-SISSOR[edit]

File Type-SISSOR (PGP1-21,22) Path File(s)
VCF-PGP1 /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22 pgp1_21and22.vcf
HAIRS-merge /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22/HAIRS fragments.chr*.sissor.txt
haplotypes /media/LTS_15T/DEJ_LTS/microfluidics_data/pgp1_21and22/haplotypes haplotype.chr*.sissor.txt

Notes:

  • * chromosomes 1 to 22