Question: Rsamtools isSupplementary argument not working
gravatar for galeoni
10 months ago by
galeoni0 wrote:

Hi to everyone,

 I'm trying to use the Rsamtools (latest version: 1.33.5) package in order to filter some .bam files.

I'm facing some problems with the isSupplementary  argument that should recognize reads flagged with the 2048 samflag within the bam file ( In particular, I've found discrepancies between the outputs of countBam() and the outputs of samtools view (from bash) that should be equals instead.

For instance, Rsamtools countBam() is returning 14036855 supplementary reads:

> param = ScanBamParam(flag = scanBamFlag(isSupplementaryAlignment = T), what = c("qname","pos","qwidth","rname"))

> countBam(input.bam, param = param)

space start end width                    file  records nucleotides
1    NA    NA  NA    NA input.bam 14036855  3423511754

while samtools view only 146529:

$ samtools view -f 2048 -c input.bam


Moreover, the total reads counts with samtools is 14036855, the very same ouput of countBam:

$ samtools view -c input.bam


I did not found discrepancies in the counts using different arguments (like isUnmappedQuery), so I think that since the isSupplementary argument is a recent implementation, could it be that there is still a bug? 

Here below the output from sessioninfo():


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/
LAPACK: /usr/lib/lapack/

 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=it_IT.UTF-8    LC_PAPER=it_IT.UTF-8       LC_NAME=C                 

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] hwriter_1.3.2        Rsamtools_1.33.5     Biostrings_2.48.0    XVector_0.20.0       GenomicRanges_1.32.7 GenomeInfoDb_1.16.0 
[7] IRanges_2.14.12      S4Vectors_0.18.3     BiocGenerics_0.26.0 

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1              Rcpp_0.12.19                lattice_0.20-35             digest_0.6.18              
 [5] plyr_1.8.4                  backports_1.1.2             acepack_1.4.1               RSQLite_2.1.1              
 [9] ggplot2_3.0.0               pillar_1.3.0                zlibbioc_1.26.0             rlang_0.2.2                
[13] lazyeval_0.2.1              rstudioapi_0.8              data.table_1.11.8           annotate_1.58.0            
[17] blob_1.1.1                  rpart_4.1-13                Matrix_1.2-14               checkmate_1.8.5            
[21] splines_3.5.1               BiocParallel_1.14.2         geneplotter_1.58.0          stringr_1.3.1              
[25] foreign_0.8-71              htmlwidgets_1.3             RCurl_1.95-4.11             bit_1.1-14                 
[29] munsell_0.5.0               DelayedArray_0.6.6          compiler_3.5.1              base64enc_0.1-3            
[33] htmltools_0.3.6             nnet_7.3-12                 SummarizedExperiment_1.10.1 tibble_1.4.2               
[37] gridExtra_2.3               htmlTable_1.12              GenomeInfoDbData_1.1.0      Hmisc_4.1-1                
[41] matrixStats_0.54.0          XML_3.98-1.16               crayon_1.3.4                bitops_1.0-6               
[45] grid_3.5.1                  xtable_1.8-3                gtable_0.2.0                DBI_1.0.0                  
[49] magrittr_1.5                scales_1.0.0                stringi_1.2.4               genefilter_1.62.0          
[53] latticeExtra_0.6-28         Formula_1.2-3               RColorBrewer_1.1-2          tools_3.5.1                
[57] bit64_0.9-7                 Biobase_2.40.0              DESeq2_1.20.0               survival_2.42-6            
[61] AnnotationDbi_1.42.1        colorspace_1.3-2            cluster_2.0.7-1             memoise_1.1.0              
[65] knitr_1.20

Thanks in advance for any suggestions and/or answers,


ADD COMMENTlink modified 10 months ago by Martin Morgan ♦♦ 23k • written 10 months ago by galeoni0
Answer: Rsamtools isSupplementary argument not working
gravatar for Martin Morgan
10 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Thank you for the report, can you try version 1.33.7, available from


now or via BiocManager::install("Rsamtools") (in devel) tomorrow afternoon?

ADD COMMENTlink written 10 months ago by Martin Morgan ♦♦ 23k

Thanks for the answer Martin and sorry for the delay in the reply,

I've tried the new version as you were suggesting (v. 1.33.7) but the discrepancy in the counts is still present. As previously reported, the isSupplementary argument seems to not affect the counts of the output. 

Thanks again for your support, 


ADD REPLYlink written 9 months ago by galeoni0

Can you provide me with a (subset) of your bam file? You can contact me at Martin.Morgan at

ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 23k

Hi Martin,

I've just found that with a fresh restart of the system, the v. 1.33.7 worked perfectly! 

Thanks again for the support,



ADD REPLYlink written 9 months ago by galeoni0
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