I am just looking for a panel of normals to use fo...
# createpanelrefss
saad khan
10/07/2025, 8:47 PMI am just looking for a panel of normals to use for my tumor data based on gatk recommendations : https://gatk.broadinstitute.org/hc/en-us/community/posts/15526698792475-Somatic-copy-number-variants-CNVs-and-Panel-of-Normals-creation and would appreciate it if someone can point me to a panel of normals for cnv. GATK has links for gs://gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz but this is for snv only i believe?
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Maxime Garcia
10/08/2025, 4:00 PMI don't think we have the GATK CNV in sarek yet, right @Rike Hanssen?
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Rike Hanssen
10/08/2025, 4:29 PMwe do not
Rike Hanssen
10/08/2025, 4:29 PMwe are doing cnvs with ascat, cnvkit and controlfreec
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Maxime Garcia
10/08/2025, 4:38 PMThat's what I thought
Maxime Garcia
10/08/2025, 4:38 PMWe are not yet doing it 🤣
Maxime Garcia
10/08/2025, 4:38 PMSoon 🔥🔥🔥