Hi! I am combining the `variants_passgeno` and `variants_anno` tables for the gold set patients (222 patients, 444 samples) and have noticed that the mutation counts and variants are the same for both the samples from the same patient? Is that right? Sorry if I am missing any information that is already provided. Could you let me know where can I find the variant information associated with the Nature 2019 article? Thanks, Ramya

Created by Ramya Madupuri madupurr
Hi Peng, Yes, ssm2_pass_call variable indicates TRUE and FALSE for each aliquot. To your second question, it depends on your research question. The prior reply and data dictionary detail the contents of this file that can help guide your approach to selecting variants. Thanks, Kevin
Follow up of this question. Dose t in the column ssm2_pass_call mean true and f means false? Only rows with a flag of t should be selected, right? Thanks for sharing the data with us! Best regards, Peng Mao
Hi Ramya, Thanks for your interest in the GLASS resource. Each row in `variants_passgeno` represents a single variant detected using multi-sample Mutect2 and is reported for a given sample. Thus, for each patient the variant information will be listed for all samples (including normal blood). Note that in the column ssm2_pass_call there is a flag indicating whether the variant was called and passed filters in single-sample Mutect2 mode. Single-sample mutation calls were overlaid on the multi-sample calls to infer whether variants were called in individual samples. This GLASS Synapse page currently represents the variant information associated with the 2019 Nature article. You will find announcements of future releases on this Synapse page and also via publications. Hope this helps, Kevin

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