ENCODE DNase I allelic imbalance data
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If you have any questions, please reach us at:
sabramov@altius.org Sergey Abramov
sboytsov@altius.org Alexandr Boytsov
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Accessing the data¶
The data is stored at https://resources.altius.org/~jvierstra/projects/encode4-allelic-imbalance-v1
The directory contains:

Metadata file: metadata.tsv
Metadata file with ENCODE IDs: metadata+encode_id.tsv
All tested variants: cav_pvalues.1010.melt.sorted.bed.gz
This readme file: README.tsv
Jupyter notebook: ENCODE DNASE I Allelic Imbalance - 2022-10-6.ipynb
phase1 genotypes (before merging): genotypes.phase1.vcf.gz
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Metadata file
ag_id - a unique identifier of a sample
idniv_id - individual genotype id. Samples with the same indiv_id have similar genotype
 (not necessarily the same cell type)
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Genotypes:
Genotypes are provided in VCF format, each sample id corresponds to ag_id in metadata file.
The columns are sorted in the same order as rows of the metadata file.
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Variants format:
Variants are stored in the bed-like format:
#chr, start, end: genomic position of the SNV, hg38 genome assembly;

ID: rsSNP ID of the SNV according to the dbSNP build 151;

ref: reference allele (A,C,G, or T, according to hg38);

alt: alternative allele;

ref_counts, alt_counts: number of reads mapped to the alleles;

sample_id: unique identifier of the sample, corresponds to ag_id in metadata file

BAD: background allelic dosage estimation at the variant. Higher BAD values correspond to the higher contribution of aneuploidy and local copy-number variants. BAD scores serve as a baseline when estimating the statistical significance and the effect size of each tested variant. BAD=1 in case of diploid and BAD=2 in case of triploid.

es: Effect size of allelic imbalance at the variant, log2. Positive values indicate imbalance favouring the reference allele. Corrected for BAD.

pval_ref, pval_alt: allele-wise P-value estimations of one-sided tests. Lower P-values indicate the preference of the corresponding allele, e.g. low pval_ref means the variant is reference imbalanced

You can download the variants in a specific region using tabix
tabix https://resources.altius.org/~jvierstra/projects/encode4-allelic-imbalance-v1/cav_pvalues.1010.melt.sorted.bed.gz ${region} > cav_pvalues_${region}.bed
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