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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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sampleSwaps Error: Zero SNPs to analyze #1044

Open tc86 opened 3 months ago

tc86 commented 3 months ago

Hi,

Thank you for developing this very useful package. I was trying to run the sampleSwaps command to check whether my bam files belong to the same cases. But while running the command, I encountered the following error

res = maftools::sampleSwaps(bams = bams, build = "hg19")
Fetching readcounts from BAM files..
Summarizing allele frequncy table..
Error in maftools::sampleSwaps(bams = bams, build = "hg19") : 
  Zero SNPs to analyze!

What could be the reason for this error, and how should I troubleshoot it? I would appreciate any help regarding this.

Session info

R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.9 (Ootpa)

Matrix products: default
BLAS/LAPACK: ~/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] maftools_2.14.0

loaded via a namespace (and not attached):
 [1] compiler_4.2.3     Matrix_1.5-4       DNAcopy_1.72.3     tools_4.2.3        RColorBrewer_1.1-3 survival_3.5-5     splines_4.2.3      grid_4.2.3         data.table_1.14.8  lattice_0.21-8
PoisonAlien commented 1 month ago

Hi,

Sorry for not getting back sooner. Do your BAM files have the chr prefix?