Changes between Version 2 and Version 3 of Ticket #1225


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Timestamp:
Jan 28, 2020, 8:41:29 AM (5 years ago)
Author:
Nicklas Nordborg
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  • Ticket #1225 – Description

    v2 v3  
    55**dbSNP updated to version 153**\\
    66It contains a lot more variants than before. Some of the fields have been removed. We no longer annotate with `CDA`, `G5` or `G5A`. See also #1222.
     7 
     8 * http://www.ensembl.info/2019/08/29/coming-soon-to-an-ensembl-near-you-dbsnp-2-0/
     9 * https://www.ncbi.nlm.nih.gov/variation/docs/snp2_human_variation_vcf/
    710
    811**COSMIC updated to version 90**\\
    9 They have made major changes to ID assignment and how samples are reported. This affected the custom scripts for calculating mutation frequencies. This was solved by matching ID+GENE from the VCF to ID+GENE in the sample mutation table. The end result should be compatible with older version of COSMIC.
     12They have made major changes to ID assignment and how samples are reported. This affected the custom scripts for calculating mutation frequencies. This was solved by matching ID+GENE from the VCF to ID+GENE in the sample mutation table. The end result should be compatible with older version of COSMIC.
     13
     14 * https://cancer.sanger.ac.uk/cosmic/variant-updates
    1015
    1116**gnomAD updated to version 2.1.1**\\
    … …  
    1520 * Genomes: AF, AF_female, AF_male, AF_nfe
    1621
     22 * https://gnomad.broadinstitute.org/about
     23 * https://macarthurlab.org/2018/10/17/gnomad-v2-1/
     24 * https://gnomad.broadinstitute.org/faq
     25
    1726**Swegen updated to version 20180409**\\
    1827We decided to use the newer hg38 version (`swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz`) instead of the hg19 version (`swegen_frequencies_hg19_20180409.tar`).