Daniel:Notebook/Haplotyping/DataMap

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Revision as of 21:33, 9 December 2015 by >Djacobse (→‎Data Update Dec. 2015)
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Data Map

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

Reference Data

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

The reference data was processed in several steps.

  1. Read in reference data and merge using 2/3 voting method (If site was called heterozygous in 2/3 cell lines)
    1. M code
  2. Convert the data to hg19 to be consistent with the other data

Data Update Dec. 2015

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

Hi-C Data

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

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

PGP1-21

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

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

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