Variant Calling used in ABB project

This dataset has two Variants Files in VCF format used in ABB project (https://github.com/Francesc-Muyas/ABB). One has the variants found in a Rare Variant Association Study performed in CLL patients. This has 1217 samples represented. The other variant file has 209 SNPs predicted in 10 samples by GATK HaplotypeCaller and selected for Sanger Sequencing Validation. Raw reads were aligned against the Human Reference genome (Hg19) with BWA mem and variants were obtained using GATK HaplotypeCaller.

1217 samples
DAC: EGAC00001000916

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ABB Policy

For research only. There are two vcf files. One of them has the significant variants found in a RVAS analysis (CLL - Chronic lymphocytic leukemia). The other, has variants called by GATK HC and selected for a posterior Sanger Sequencing validation.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID	Study Title	Study Type
EGAS00001003027	Allele Balance Bias Identifies Systematic Genotyping Errors and False Disease Associations	Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID	File Type	Size
EGAF00002013046	vcf.gz	43.7 kB
EGAF00002013047	vcf.gz	4.0 MB
2 Files (4.1 MB)