feat: update cnvkit pons #1465
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feat: update cnvkit pons #1465
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## deduplicate_with_umi #1465 +/- ##
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## Added - padding of bed-regions for CNVkit to minimum 100 base
…SAMIC into update_cnvkit_pons
ivadym
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Jul 30, 2024
BALSAMIC/snakemake_rules/variant_calling/somatic_cnv_tumor_normal_tga.rule
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…ALSAMIC into deduplicate_with_umi
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Description
THIS PR IS WAS BLOCKED BY THIS: https://github.com/Clinical-Genomics/target_capture_bed/issues/133
Now solved by this: #1469
With the change to the BAM files in the TGA workflows to start using UMIs for removing duplicates we will need to rebuild the PONs for all TGA workflows:
At the same time there are issues with the current GMSmyeloid PON with reports of noisy results which may be due to the fact that the PON was built using tumor samples and with a mix of samples from an earlier version of the panel. So while re-building the PON we might take the time to choose better samples if any are available.
Also for the other panels it would be good to re-evaluate which samples we have and can use to make sure that we're using samples that are up to date with our methods.
Finally, we can see if there are any other panels available for which we have enough samples to create a PON. Such as the one mentioned here: #1460
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Added google-sheet here: https://docs.google.com/spreadsheets/d/18vs_2MKk-IyByjGMqEptdSlfcn9mB9bbpx6DahCA_a4/edit?gid=1393363517#gid=1393363517
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.hkfile)Clinical Genomics Stockholm
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Panel of Normal specific criteria
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