NA12878 WES Benchmark dataset

<p>This dataset makes available the UCSC Genome Browser (genome.ucsc.edu) GRCh37 genome build public session <strong>NA12878 WES Benchmark </strong>files in a single dataset so that these files can be used in other applications or genome browsers such as IGV.&nbsp;</p> <p>The <a href="https://usegalaxy.org/u/erinija/p/omim-genes-in-na12878-wes-benchmark">&quot;Procedure and datasets to cross-reference OMIM genes with the genomic regions of interest&quot;</a>&nbsp; Galaxy page&nbsp; on&nbsp; <strong>usegalaxy.org</strong> server&#39;s&nbsp;<em><strong>Shared Data Pages</strong></em> describes&nbsp;practical procedure and several possible use cases for this data set. This page can be accessed freely by users logged into their accounts on usegalaxy.org.&nbsp; Please register if you don&#39;t have an account on usegalaxy.org Galaxy server. &nbsp;</p> <p>All&nbsp; genomic variant calls in&nbsp; all VCF files of this data set were decomposed and normalized with vt. This dataset contains:&nbsp;</p> <ol> <li>Genome in a bottle (GIAB)&nbsp;version 3.3.2 high confidence (HC)&nbsp; variant calls and genomic regions for HapMap individual NA12878 : <ol> <li>GIAB_v3.3.2_NA12878-decomposed-normalized.vcf.gz</li> <li>GIAB_v3.3.2_NA12878-decomposed-normalized.vcf.gz.tbi</li> <li>GIAB_v3.3.2_NA12878_HC_regions.bed</li> </ol> </li> <li>HapMap individual NA12878 WES variant calls (VCF) and capture regions (BED) from diagnostic laboratories : <ul> <li>ARUP whole exome sequencing data (HiSeq 2000) publically available from NCBI GeT-RM Browser <ol> <li>converted_ARUP_NA12878_Exome-decomposed-normalized.vcf.gz</li> <li>converted_ARUP_NA12878_Exome-decomposed-normalized.vcf.gz.tbi</li> <li>&nbsp;ARUP_SeqCap_EZ_Exome.bed</li> </ol> </li> <li>UCSF whole exome sequencing data (HiSeq 2500) publically available from NCBI GeT-RM Browser <ol> <li>converted_UCSF_NA12878_WES_Agilent_V4_Custom-decomposed-normalized.vcf.gz</li> <li>converted_UCSF_NA12878_WES_Agilent_V4_Custom-decomposed-normalized.vcf.gz.tbi</li> <li>UCSF_WES_Agilent_V4_Custom.bed</li> </ol> </li> <li>Whole exome data (NextSeq 500) sequenced in CHEO diagnostic laboratory <ol> <li>CHEO_NA12878_WES_S1dataset.vcf.gz</li> <li>CHEO_NA12878_WES_S1dataset.vcf.gz.tbi</li> <li>Agilent_CRE_v2.bed</li> </ol> </li> </ul> </li> <li>Genomic coordinates (BED) of OMIM genes for which a molecular basis of the associated disease is known (as of September 2019) : <ul> <li>Omim_Genes.bed&nbsp;</li> </ul> </li> </ol>