SNP Base pair calls for NA12878 and NA12877

[bradfordok]

Hello, I need some technical assistance. I have a genotyping results for a number of SNPs (rs.....) and associated allele 1 and allelle 2 base calls for NA12878 and NA12877. I'm trying to find where the data exists to ensure I have concordance. How do I obtain this data for comparisons of my illumina genotyping of these snps with data that exists on platinum genomes? Is there a file you can point me to?

[eberle]

There are some instructions on downloading the data if you go to https://github.com/Illumina/PlatinumGenomes and read the text farther down the page. If you prefer, you can directly browse the data here https://illumina.github.io/PlatinumGenomes/. The vcf files will contain the truth SNPs and indels for NA12877 and NA12878 and the confident regions bed files summarizes the coordinates where we believe the GT is known. If it's in a confident region but not in the vcf file then the site should be homozygous for the reference allele.

[bradfordok]

Can the .vcf files be opened in notepad, or what software do I need? Kindly, Rebecca Bradford, M.B.A, M.S., PMP® SR DIRECTOR, GOVERNMENT PROGRAMS BEI RESOURCES PRINCIPAL INVESTIGATOR ATCC FEDERAL SOLUTIONS 10801 University Boulevard Manassas, VA 20110-2209 Tel: (703) 365-2700 ext. 2846 Fax: (703) 365-2701 Email: ***@***.*** From: eberle ***@***.***> Sent: Friday, October 08, 2021 11:34 AM To: Illumina/PlatinumGenomes ***@***.***> Cc: Bradford, Rebecca ***@***.***>; Author ***@***.***> Subject: Re: [Illumina/PlatinumGenomes] SNP Base pair calls for NA12878 and NA12877 (#14) There are some instructions on downloading the data if you go to https://github.com/Illumina/PlatinumGenomes<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Illumina_PlatinumGenomes&d=DwMCaQ&c=dcFnI-8Ri3NVXdqjME8ydA&r=eA3zTJxwXCmlnZgIbqMroY0lnEHoS938ZSXCfWXjknU&m=S9IJEBtBM6khW5BeNFSNlVMRTMtSlN99ROrcLENuiw83Yt0PAXfIKQlBu3SShudV&s=9PDhIiL5zbRrKVzPQDCSrKWFYuT3Yo5Lo_2Dgu-2kks&e=> and read the text farther down the page. If you prefer, you can directly browse the data here https://illumina.github.io/PlatinumGenomes/<https://urldefense.proofpoint.com/v2/url?u=https-3A__illumina.github.io_PlatinumGenomes_&d=DwMCaQ&c=dcFnI-8Ri3NVXdqjME8ydA&r=eA3zTJxwXCmlnZgIbqMroY0lnEHoS938ZSXCfWXjknU&m=S9IJEBtBM6khW5BeNFSNlVMRTMtSlN99ROrcLENuiw83Yt0PAXfIKQlBu3SShudV&s=HwPtRnVSvW5FT6uCN1aUG3XKGHh8ic79h301P8CCQGg&e=>. The vcf files will contain the truth SNPs and indels for NA12877 and NA12878 and the confident regions bed files summarizes the coordinates where we believe the GT is known. If it's in a confident region but not in the vcf file then the site should be homozygous for the reference allele. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Illumina_PlatinumGenomes_issues_14-23issuecomment-2D938735735&d=DwMCaQ&c=dcFnI-8Ri3NVXdqjME8ydA&r=eA3zTJxwXCmlnZgIbqMroY0lnEHoS938ZSXCfWXjknU&m=S9IJEBtBM6khW5BeNFSNlVMRTMtSlN99ROrcLENuiw83Yt0PAXfIKQlBu3SShudV&s=oxCe_4kH7ZE-_q2MObIF2muF-NxOG9rzbWDL19FrWzk&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AV62EAKDJRY5KDG6TWHJDKLUF4FODANCNFSM5FT25E5A&d=DwMCaQ&c=dcFnI-8Ri3NVXdqjME8ydA&r=eA3zTJxwXCmlnZgIbqMroY0lnEHoS938ZSXCfWXjknU&m=S9IJEBtBM6khW5BeNFSNlVMRTMtSlN99ROrcLENuiw83Yt0PAXfIKQlBu3SShudV&s=LlIFcHO6PBtNs9qWjDoVi5b8I4vhggBeNAbIWy1fN_c&e=>. Triage notifications on the go with GitHub Mobile for iOS<https://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=dcFnI-8Ri3NVXdqjME8ydA&r=eA3zTJxwXCmlnZgIbqMroY0lnEHoS938ZSXCfWXjknU&m=S9IJEBtBM6khW5BeNFSNlVMRTMtSlN99ROrcLENuiw83Yt0PAXfIKQlBu3SShudV&s=A2uDLAnaT4WtARgUB66zxLU2mJElLYzx4-CCJ8ajvZQ&e=> or Android<https://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=dcFnI-8Ri3NVXdqjME8ydA&r=eA3zTJxwXCmlnZgIbqMroY0lnEHoS938ZSXCfWXjknU&m=S9IJEBtBM6khW5BeNFSNlVMRTMtSlN99ROrcLENuiw83Yt0PAXfIKQlBu3SShudV&s=sMpfcL2td9o7wVVBL-2lCqLxhL95i-81BqaRd7yAL1I&e=>.