Encountered an error while retrieving TCGA Simple Nucleotide Variation data using GDCprepare

[AlexanderXie98]

I encountered an issue when using GDCprepare fromTCGAbiolinks version 2.30.0 to retrieve Simple Nucleotide Variation data for TCGA-CESC. The error message is as follows:

dplyr::bind_rows(res, .id = .id)
Error in `dplyr::bind_rows()`: ! Can't combine `..20$Tumor_Seq_Allele2` <character> and `..21$Tumor_Seq_Allele2` <logical>.

Upon reviewing the source code, I have identified that this error is triggered by purrr::map_dfr(...)under readSimpleNucleotideVariationMaf(files). I am uncertain about how to resolve this issue and would greatly appreciate any help.

Thank you very much!

Best regards, Alexander

[sigven]

I have encountered the same issue with GDCprepare (v2.30.0) for the TCGA-CHOL cohort:

Can't combine..45$Tumor_Seq_Allele2<character> and..46$Tumor_Seq_Allele2<logical>

[tiagochst]

Thank you for the bug report.

Please, could you try updating to the latest version in github please: BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

On Sun, Nov 5, 2023 at 8:11 AM Sigve Nakken @.***> wrote:

I have encountered the same issue with GDCprepare (v2.30.0) for the TCGA-CHOL cohort:

Can't combine ..45$Tumor_Seq_Allele2 and..46$Tumor_Seq_Allele2

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[sigven]

Thanks, works now:-)

[Hawyoo]

TCGA-BRCA works now, too :-)

[elsiebrownn]

Thank you for the bug report. Please, could you try updating to the latest version in github please: BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") …

Hi, I'm having the same issue for BRCA and LAML - using v2.31.2