alias: HG003: NA24149
title: GIAB Illumina 10X Genomics-  HG003: NA24149
design: All data provided here (along w/ additional tools to visualize the data) are also available  at: http://software.10xgenomics.com/giab2015  I. Samples Provided Included in this data release are raw data and results from 4 different samples: (1) NA12878 (Pilot genome) (2) NA24385 (Ashkenazim trio son) (3) NA24149 (Ashkenazim trio father) (4) NA24143 (Ashkenazim trio mother)  II. Sample Preparation and Sequencing All DNA was freshly extracted from cells obtained from Coriell, using a modified version of the Qiagen MagAttract protocol (as described in the GemCode User Guide Rev B).  10X GemCode libraries were prepared according to the standard GemCode protocol (as described in the GemCode User Guide Rev B). Briefly, 1.2ng of input molecules were partitioned using a microfluidic chip into > 200,000 molecular reactors to extend DNA fragments and introduce a 14bp partition-specific barcode, creating Linked-Reads.  Libraries were sequenced on a HiSeq2500 (using either High Output v4 or Rapid Run v1 chemistry) to the following short-read depths: NA12878: 34X NA24385: 25X NA24149: 22X NA24143: 24X  Details on the GemCode technology can be found at: http://10xgenomics.com  III. Data Processing Long Ranger software was used to perform barcode-aware analysis including detection and phasing of structural variants, and phasing of SNPs and small indels from publicly available Genome in a Bottle VCFs.  Detailed documentation on the GemCode Long Ranger software can be found at: http://software.10xgenomics.com  VCF files used were: NA12878: RTG â€˜SPâ€™ file:  (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/analysis/variant_calls/RTG/phasing_annotated.vcf.gz) NA24385: CallsIn2Technologies (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_CallsIn2Technologies_05182015/HG002-multiall-fullcombine.vcf.gz) NA24149: CallsIn2Technologies (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_CallsIn2Technologies_05182015/HG003-multiall-fullcombine.vcf.gz) NA24143: CallsIn2Technologies (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_CallsIn2Technologies_05182015/HG004-multiall-fullcombine.vcf.gz)  IV. Files and File Formats: The following files are provided for each dataset above: (i) BAM (and index): Contains aligned and position-sorted reads along with associated barcodes. (ii) VCF (and index): Contains phasing calls for SNPs and small indels (along with barcode-support) (iii) BEDPE: Contains large-scale (~50Kb or greater and inter-chromosomal) structural variant calls.  This includes multiple types of SVs. (iv)TSV: Contains phasing calls for the above structural variant calls.  Detailed documentation on formats for the above files can be found at: http://software.10xgenomics.com
identifiers.namespace: NCBI
identifiers.id: HG003: NA24149