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Title: Variant Recalling (GATK) from Whole Exome Sequencing data for 2415 families in SSC Collection      
dateReleased:
01-30-2017
privacy:
information not avaiable
aggregation:
instance of dataset
dateCreated:
02-04-2015
refinement:
curated
ID:
doi:10.15154/1169195
creators:
Krumm, N
Eichler, E
availability:
available
types:
other
description:
Whole Exome Sequencing has been completed for ~ 2500 families from the Simons Simplex Collection. Sequencing was performed at three individual sequencing centers with original data submitted to NDAR Collections 1878, 1895, and 1936; subsets of these data have been analyzed by various methods and published. This study represents an effort to call and annotate SNPs and Indels on data from all three collections in a uniform manner using the latest toolchains and algorithms available. Variant calls from this study were generated using GATK, Famseq, and some custom scripts; annotation was provided by SnpEff, dbNSFP, and vcftools. Note that variants were called in batches with ~ 20 families per batch. Complete methods, including source code for pipeline and custom scripts can be found at: https://github.com/nkrumm/asd-jre-public The data package for this study represents the genomics_subject02, genomics_sample03 structures which include annotated and un-annotated VCF files for each family. Another NDAR Study (349) is available with VCF files generated using FreeBayes (https://ndar.nih.gov/study.html?id=349), and the complete set of BAM files used for variant calling are available in NDAR Study 334 (https://ndar.nih.gov/study.html?id=334)
accessURL: https://doi.org/10.15154/1169195
storedIn:
NIMH Data Archives
qualifier:
not compressed
format:
HTML
accessType:
landing page
authentication:
none
authorization:
none
abbreviation:
NIH
homePage: http://www.nih.gov/
ID:
SCR:011417
name:
National Institutes of Health
abbreviation:
NIMH
homePage: http://www.nimh.nih.gov/
ID:
SCR:011431
name:
National Institute of Mental Health

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