read.maf: duplicate variants removed?

[complexgenome]

Hello there,
I'm using maftools to work on a cohorts' maf.

I read them and merge using maftools' utility. When the merge is complete I get message that XX number of duplicate variants are removed.

I'd like to know what's causing it to remove. As I understand there are different samples across in the cohort; they may have same SNP but why are they excluded and are considered duplicates?

mafs = data.table::rbindlist(l = mafs_datatable, use.names = TRUE, fill = TRUE, idcol = "Source_MAF") 

 mafs_read = maftools::read.maf(maf = mafs) 

Validating
--Removed 124759 duplicated variants
--Non MAF specific values in Variant_Classification column:
START_CODON_SNP
DE_NOVO_START_OUT_FRAME
DE_NOVO_START_IN_FRAME -
Silent variants: 29303 -
Summarizing --
Possible FLAGS among top ten genes:
TTN MUC16 OBSCN USH2A
-Processing clinical data
--Missing clinical data
-Finished in 2.638s elapsed (22.1s cpu)

maftools v2.18.0
R 4.3.2 (2023-10-31)

Let me know if any other details are needed.

[PoisonAlien]

Hi,

Variants are considered duplicates if they occur more than once within the same sample. Here is how they are identified an removed.

It might be the case that the same variant is being assigned to multiple transcripts - and hence are identified as duplciates. You can turn off with removeDuplicatedVariants = FALSE in read.maf()

I hope this helps.