Data Release notes for the workspace

1000 Genomes 3202 phase 3, Update May 23, 2023

From March 8, 2023 to May 8, 2023, the following files below were temporarily unavailable. As of May 8, 2023, these files have been restored. 

HG00257.final.cram
HG00369.final.cram
HG00657.final.cram
HG00684.final.cram
HG01079.final.cram
HG01110.final.cram
HG01122.final.cram
HG01491.final.cram
HG01697.final.cram
HG01777.final.cram
HG01976.final.cram
HG02164.final.cram
HG02312.final.cram
HG02380.final.cram
HG02512.final.cram
HG02557.final.cram
HG02681.final.cram
HG02769.final.cram
HG03063.final.cram
HG03563.final.cram
HG03844.final.cram
HG03898.final.cram
HG03937.final.cram
HG04141.final.cram
NA18912.final.cram
NA19060.final.cram
NA19238.final.cram
NA19360.final.cram
NA19474.final.cram
NA20790.final.cram
NA21126.final.cram
HG00408.final.cram
HG00639.final.cram
HG01096.final.cram
HG01529.final.cram
HG02821.final.cram
HG03047.final.cram
HG03487.final.cram
NA18487.final.cram
NA18500.final.cram
NA20279.final.cram
HG01141.haplotypeCalls.er.raw.vcf.gz
NA10830.haplotypeCalls.er.raw.vcf.gz
NA18863.haplotypeCalls.er.raw.vcf.gz


1000 Genomes 3202 phase 3 panel samples sequenced to high coverage
==================================================================

This policy refers to 30x Illumina NovaSeq sequencing of 3202 samples from the 1000 Genomes project phase 3 sample set, along with 698 family members that complete trios in the phase 3 data . These data were generated at the New York Genome Center with funds provided by NHGRI Grant 3UM1HG008901. Please email service@nygenome.org with questions or interest in undertaking collaborative analysis of this dataset. All cell lines were obtained from the Coriell Institute for Medical Research and were consented for full public release of genomic data. Please see Coriell (https://www.coriell.org) for more information about specific cell lines. The following cell lines/DNA samples were obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research: [NA06984, NA06985, NA06986, NA06989, NA06994, NA07000, NA07037, NA07048, NA07051, NA07056, NA07347, NA07357, NA10847, NA10851, NA11829, NA11830, NA11831, NA11832, NA11840, NA11843, NA11881, NA11892, NA11893, NA11894, NA11918, NA11919, NA11920, NA11930. NA11931, NA11932, NA11933, NA11992, NA11994, NA11995, NA12003, NA12004, NA12005, NA12006, NA12043, NA12044, NA12045, NA12046, NA12058, NA12144, NA12154, NA12155, NA12156, NA12234, NA12249, NA12272, NA12273, NA12275, NA12282, NA12283, NA12286, NA12287, NA12340, NA12341, NA12342, NA12347, NA12348, NA12383, NA12399, NA12400, NA12413,, NA12414, NA12489, NA12546, NA12716, NA12717, NA12718, NA12748, NA12749, NA12750, NA12751, NA12760, NA12761, NA12762, NA12763, NA12775, NA12776, NA12777, NA12778, NA12812, NA12813, NA12814, NA12815, NA12827, NA12828, NA12829, NA12830, NA12842, NA12843, NA12872, NA12873, NA12874, NA12878, NA12889, NA12890, NA12376, NA10838, NA12329, NA10852, NA10840, NA12386, NA12864, NA12801, NA12344, NA10861, NA07029, NA12753, NA12832, NA12485, NA12802, NA12739, NA10856, NA10845, NA12818, NA10831, NA12766, NA10864, NA10843, NA12877, NA12335, NA12817, NA12752, NA12767, NA10855, NA12707, NA10857, NA10839, NA12740, NA10837, NA10836, NA07348, NA11993, NA12057, NA11839, NA06993, NA07014, NA06995, NA12146, NA12865, NA10859,
NA06991, NA12336, NA10860, NA12145, NA07045, NA07349, NA07031, NA07345, NA12891, NA07055, NA07435, NA10835, NA12274, NA12875, NA10842, NA12239, NA10830, NA12056, NA11917, NA12892, NA06997, NA07022, NA12264, NA11891, NA07034, NA12248, NA10865, , NA10863, NA10854, NA11882, NA07346, NA07019, NA12343, NA10846].

If using this data please acknowledge that: These data were generated at the New York Genome Center with funds provided by NHGRI Grant 3UM1HG008901-03S1. Additionally, if data from any of the cell lines listed were used, then they should be cited specifically as coming from NIGMS.

For more general information about the consent for the samples in this data set, please see http://www.internationalgenome.org/about#g1k_data_reuse.

For general enquiries, please contact info@1000genomes.org.


==================================================================

1000 Genomes Processing README

This README contains information relating to data associated with the 1000 Genomes 
resequencing done at New York Genome Center.
Alignment, post-processing and variant calling
Alignment and post-processing are performed exactly as outlined by the Center for
Common Disease Genomics project: https://github.com/CCDG/PipelineStandardization/blob/master/PipelineStandard.md .
Programs and reference data
The data was aligned to the reference genome using the following programs and reference 
datasets:
1. BWA-MEM bwakit-0.7.15
2. Samtools-1.3.1
3. Picard-2.4.1
4. GATK-3.5-0
5. Resource files - All the resource files used in the analysis can be obtained here: 
https://console.cloud.google.com/storage/browser/genomics-publicdata/resources/broad/hg38/v0/ .
Reference genome: GRCh38 with alternative sequences, plus decoys and HLA
The reference genome that the data was aligned to can be obtained here: 
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome
/GRCh38_full_analysis_set_plus_decoy_hla.fa

==================================================================

Analysis work is being done by a number of groups, working toward variant calling, including identification of structural variation.

Initial analysis has been done by NYGC, including aligning the data to GRCh38, creating the CRAMs in ENA. The document [NYGC_b38_pipeline_description.pdf](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_cov/NYGC_b38_pipeline_description.pdf) contains a description of that analysis work and details of the alignment pipeline.

Should you have questions about this data please contact info@1000genomes.org
 Platform: AnVIL

ANVIL_1000G_high_coverage_2019

Description

Dataset Details