test_ctDNA not working with hg19 NCBI BAM file

[zahrahaider]

Hi,

Thanks for a great tool! I am trying to use test_ctDNA on bam files from targeted panel sequencing data and with BAM files aligned to RefSeq: NCBI GRCH37 Reference Sequence. Even after changing the seqname style of the BSgenome.Hsapiens.UCSC.hg19 from UCSC to NCBI, I kept getting the error: "Error: Chromosomes in bam file don't match the specified reference".
I saw that the culprit chromosomes were these unlocalized sequences GL00* when I ran the get_bam_chr() function. These sequences failed to map in BSgenome when I switched from UCSC to NCBI.
Is there a way to skip the chromosomes in the BAM file that do not match the reference? Could that be added as a parameter to the test_ctDNA function?

Below is the code and the sessionInfo():

#To make BSgenome.Hsapiens.UCSC.hg19 package compatible, I first changed the seqname style as follows:
library(BSgenome.Hsapiens.UCSC.hg19)

#change ref genome seq style from Ucsc (chr) to NCBI to match the bam files 

hg19 <- BSgenome.Hsapiens.UCSC.hg19
seqlevelsStyle(hg19) <- "NCBI"

#test ctDNA

test_pos_mrd<-test_ctDNA(bam="panel_data/bam_files/P05.preop.subset.bam",mutations = mutations_df[mutations_df$patient_id=="P05",c("CHROM","POS","REF","ALT")],targets = target,reference = hg19,informative_reads_threshold = 100)

Error: Chromosomes in bam file don't match the specified reference

#check the chromosomes in BAM file
> get_bam_chr("panel_data/bam_files/P05.preop.subset.bam")
 [1] "1"          "2"          "3"          "4"          "5"         
 [6] "6"          "7"          "8"          "9"          "10"        
[11] "11"         "12"         "13"         "14"         "15"        
[16] "16"         "17"         "18"         "19"         "20"        
[21] "21"         "22"         "X"          "Y"          "MT"        
[26] "GL000207.1" "GL000226.1" "GL000229.1" "GL000231.1" "GL000210.1"
[31] "GL000239.1" "GL000235.1" "GL000201.1" "GL000247.1" "GL000245.1"
[36] "GL000197.1" "GL000203.1" "GL000246.1" "GL000249.1" "GL000196.1"
[41] "GL000248.1" "GL000244.1" "GL000238.1" "GL000202.1" "GL000234.1"
[46] "GL000232.1" "GL000206.1" "GL000240.1" "GL000236.1" "GL000241.1"
[51] "GL000243.1" "GL000242.1" "GL000230.1" "GL000237.1" "GL000233.1"
[56] "GL000204.1" "GL000198.1" "GL000208.1" "GL000191.1" "GL000227.1"
[61] "GL000228.1" "GL000214.1" "GL000221.1" "GL000209.1" "GL000218.1"
[66] "GL000220.1" "GL000213.1" "GL000211.1" "GL000199.1" "GL000217.1"
[71] "GL000216.1" "GL000215.1" "GL000205.1" "GL000219.1" "GL000224.1"
[76] "GL000223.1" "GL000195.1" "GL000212.1" "GL000222.1" "GL000200.1"
[81] "GL000193.1" "GL000194.1" "GL000225.1" "GL000192.1"

##session_info

R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS/LAPACK: /Users/zahra/.conda/envs/R/lib/libopenblasp-r0.3.23.dylib;  LAPACK version 3.11.0

locale:
[1] C/UTF-8/C/C/C/C

time zone: Europe/Stockholm
tzcode source: system (macOS)

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

other attached packages:
 [1] data.table_1.14.10                GenomicAlignments_1.38.0         
 [3] SummarizedExperiment_1.32.0       Biobase_2.60.0                   
 [5] MatrixGenerics_1.14.0             matrixStats_1.2.0                
 [7] Rsamtools_2.16.0                  BSgenome.Hsapiens.UCSC.hg19_1.4.3
 [9] BSgenome_1.70.1                   rtracklayer_1.62.0               
[11] BiocIO_1.12.0                     Biostrings_2.68.1                
[13] XVector_0.40.0                    GenomicRanges_1.52.1             
[15] GenomeInfoDb_1.36.4               IRanges_2.34.1                   
[17] S4Vectors_0.38.2                  BiocGenerics_0.46.0              
[19] plyr_1.8.9                        ggplot2_3.4.4                    
[21] dplyr_1.1.4                       tidyr_1.3.0                      
[23] purrr_1.0.2                       ctDNAtools_0.4.1                 

loaded via a namespace (and not attached):
 [1] utf8_1.2.4              generics_0.1.3          SparseArray_1.2.2      
 [4] bitops_1.0-7            lattice_0.22-5          magrittr_2.0.3         
 [7] grid_4.3.2              Matrix_1.6-4            restfulr_0.0.15        
[10] fansi_1.0.6             scales_1.3.0            XML_3.99-0.16          
[13] codetools_0.2-19        abind_1.4-5             cli_3.6.2              
[16] rlang_1.1.2             crayon_1.5.2            munsell_0.5.0          
[19] DelayedArray_0.28.0     withr_2.5.2             yaml_2.3.8             
[22] S4Arrays_1.2.0          tools_4.3.2             parallel_4.3.2         
[25] BiocParallel_1.34.2     colorspace_2.1-0        GenomeInfoDbData_1.2.10
[28] assertthat_0.2.1        vctrs_0.6.5             R6_2.5.1               
[31] lifecycle_1.0.4         zlibbioc_1.46.0         pkgconfig_2.0.3        
[34] pillar_1.9.0            gtable_0.3.4            glue_1.6.2             
[37] Rcpp_1.0.11             tibble_3.2.1            tidyselect_1.2.0       
[40] rjson_0.2.21            compiler_4.3.2          RCurl_1.98-1.13