Daniel:Notebook/Haplotyping/DataMap: Difference between revisions
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##[[File:Vcfmergingfiles.mcode.completegenomics.zip|M code]] | ##[[File:Vcfmergingfiles.mcode.completegenomics.zip|M code]] | ||
#Convert the data to hg19 to be consistent with the other data | #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. | |||
*[https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=0 Hi-C Data Map] | |||
*BAC Data Map | |||
*LFR Data Map | |||
*BAC+Hi-C Data Map | |||
*LFR + Hi-C Data Map | |||
*BAC+Hi-C+LFR Data Map | |||
Revision as of 23:16, 7 December 2015
Data Map
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.
- Read in reference data and merge using 2/3 voting method (If site was called heterozygous in 2/3 cell lines)
- 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.
- Hi-C Data Map
- BAC Data Map
- LFR Data Map
- BAC+Hi-C Data Map
- LFR + Hi-C Data Map
- BAC+Hi-C+LFR 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