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<TITLE> [dbsnp-announce] ANNOUNCEMENT: dbSNP Human Build 150 Double in Size to 324 Million Reference SNP (rs)
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<H1>[dbsnp-announce] ANNOUNCEMENT: dbSNP Human Build 150 Double in Size to 324 Million Reference SNP (rs)</H1>
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<B>Public announcements regarding dbSNP</B>
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<A HREF="mailto:dbsnp-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5Bdbsnp-announce%5D%20ANNOUNCEMENT%3A%20dbSNP%20Human%20Build%20150%20Double%20in%20Size%0A%20to%20324%20Million%20Reference%20SNP%20%28rs%29&In-Reply-To=%3Cmailman.10007.1491527003.18787.dbsnp-announce%40ncbi.nlm.nih.gov%3E"
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TITLE="[dbsnp-announce] ANNOUNCEMENT: dbSNP Human Build 150 Double in Size to 324 Million Reference SNP (rs)">dbsnp-announce at ncbi.nlm.nih.gov
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</A><BR>
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<I>Thu Apr 6 21:03:22 EDT 2017</I>
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<PRE>dbSNP human build 150 for both GRCh38.p7 and GRCh37.p13 assemblies is now available. This build includes new submissions from TopMed (<A HREF="https://www.nhlbi.nih.gov/research/resources/nhlbi-precision-medicine-initiative/topmed">https://www.nhlbi.nih.gov/research/resources/nhlbi-precision-medicine-initiative/topmed</A>) and HLI (<A HREF="http://www.humanlongevity.com/">http://www.humanlongevity.com/</A>) which more than double the number of available dbSNP reference SNP (rs) from 154 million to 324 million. The TopMed data included allele frequency data for 163M rs.
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Build Summary
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=============
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Organism: Homo sapiens
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Tax_id: 9606
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Common_name: human
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Assembly: GRCh38.p7 (GCF_000001405.33)
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Total_ss_cnt: 907237763
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Total_rs_cnt: 325658303
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New_ss_cnt: 349297803
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New_rs_cnt: 171451449
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FTP: <A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606</A>
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Entrez: <A HREF="http://www.ncbi.nlm.nih.gov/snp/?term=txid9606">http://www.ncbi.nlm.nih.gov/snp/?term=txid9606</A>
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====================================================================================
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IMPORTANT NOTIFICATION FOR SQL DATABASE USERS
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Beginning early next year 2018 dbSNP will no longer provide relational database table dumps on the FTP site (<A HREF="ftp://ftp.ncbi.nlm.nih.gov/snp/human_9606/database">ftp://ftp.ncbi.nlm.nih.gov/snp/human_9606/database</A>) or any general SQL support for future build releases. Instead, the dbSNP data will be made available as a cumulative file of RefSNP objects in the JSON format which are available now for user's to begin their migration and testing. Please see here for more details (<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/ALERT_README.txt">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/ALERT_README.txt</A>).
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====================================================================================
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Build Notes:
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* Submission from HLI were submitted on GRCh38 coordinates and because dbSNP pipeline does not support mapping backward to previous assembly the rs for these will not appear in the VCF based on GRCh37. We will investigate remapping from GRCh38 to GRCh37 and will provide updates.
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* Due the unexpected increase in the volume of human data and limitations in our systems, dbSNP had to take two temporary actions for this release:
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1. The annotation track "dbSNP Build 150 (Homo sapiens Annotation Release 108) all data" for RefSeq genomic sequences will be limited to variants in the gene regions only. This only affect tracks on NCBI Sequence Viewer and not reporting in dbSNP FTP files or on Reference SNP pages. We will investigate upgrading our systems to restore complete annotation across the genome and will provide updates.
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2. Entrez search are only available for human build 150 and a limited number of organisms from previous builds including mouse, rat, cow, and pig. We will try to restore other organisms in the next two weeks and provide updates.
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* TopMed submitted allele frequency are available in VCF on the FTP with the INFO tag 'TOPMED'.
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##INFO=<ID=TOPMED,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on TOPMED, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMED minor allele is the second largest value in the list.">
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GRCh37.p13:
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF</A>
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GRCh38.p7:
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF</A>
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Please email <A HREF="http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce">snp-admin at ncbi.nlm.nih.gov</A> for any questions and comments.
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Regards,
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dbSNP Production Team
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