seqGDS2VCF error after using seqMerge

[gustavahlberg]

After having merged some gds files I am getting an error with seqGDS2VCF due to seqSummary()
This stems from the .summary_filter() function were the attributes of the merged gds seems to somehow get twisted.

traceback()
4: stop(gettextf("arguments imply differing number of rows: %s",                                                                                                                                           
        paste(unique(nrows), collapse = ", ")), domain = NA)                                                                                                                                                
 3: data.frame(ID = id, Description = dp, stringsAsFactors = FALSE)                                                                                                                                         
 2: .summary_filter(gdsfile, check, verbose)                                                                                                                                                                
 1: seqSummary(gdsmerged, check = "none", verbose = FALSE)

Filter attribute in one of the original gds files

 $R.class                                                                                                                                                                                                   
 [1] "factor"                                                                                                                                                                                               
                                                                                                                                                                                                            
 $R.levels                                                                                                                                                                                                  
 [1] "PASS"        "MONOALLELIC"                                                                                                                                                                            
                                                                                                                                                                                                            
 $Description                                                                                                                                                                                               
 [1] "All filters passed"                                                                                                                                                                                   
 [2] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                 
                                                                                                                                                                                                            
 $md5                                                                                                                                                                                                       
 [1] "dde0f98a641ade2203cb5ab84d037576"  

Filter attribute in the merged gds

 $Description                                                                                                                                                                                               
  [1] "All filters passed"                                                                                                                                                                                  
  [2] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
  [3] "All filters passed"                                                                                                                                                                                  
  [4] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
  [5] "All filters passed"                                                                                                                                                                                  
  [6] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
  [7] "All filters passed"                                                                                                                                                                                  
  [8] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
  [9] "All filters passed"                                                                                                                                                                                  
 [10] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
 [11] "All filters passed"                                                                                                                                                                                  
 [12] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
 [13] "All filters passed"                                                                                                                                                                                  
 [14] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
 [15] "All filters passed"                                                                                                                                                                                  
 [16] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
 [17] "All filters passed"                                                                                                                                                                                  
 [18] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
 [19] "All filters passed"                                                                                                                                                                                  
 [20] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
 [21] "All filters passed"                                                                                                                                                                                  
 [22] "Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites"                                                                
                                                                                                                                                                                                            
 $md5                                                                                                                                                                                                       
 [1] "754cf550034a5297723ac2e7ac510f9c"

sessionInfo()
 R version 4.0.0 (2020-04-24)                                                                                                                                                                               
 Platform: x86_64-pc-linux-gnu (64-bit)                                                                                                                                                                     
 Running under: CentOS Linux 7 (Core)                                                                                                                                                                       
                                                                                                                                                                                                            
 Matrix products: default                                                                                                                                                                                   
 BLAS/LAPACK: /services/tools/intel/perflibs/2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so                                                                            
                                                                                                                                                                                                            
 locale:                                                                                                                                                                                                    
  [1] LC_CTYPE=en_US.utf-8       LC_NUMERIC=C                                                                                                                                                               
  [3] LC_TIME=en_US.utf-8        LC_COLLATE=en_US.utf-8                                                                                                                                                     
  [5] LC_MONETARY=en_US.utf-8    LC_MESSAGES=en_US.utf-8                                                                                                                                                    
  [7] LC_PAPER=en_US.utf-8       LC_NAME=C                                                                                                                                                                  
  [9] LC_ADDRESS=C               LC_TELEPHONE=C                                                                                                                                                             
 [11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C                                                                                                                                                        
                                                                                                                                                                                                            
 attached base packages:                                                                                                                                                                                    
 [1] stats     graphics  grDevices utils     datasets  methods   base                                                                                                                                       
                                                                                                                                                                                                            
 other attached packages:                                                                                                                                                                                   
 [1] GMMAT_1.3.1        SeqVarTools_1.28.0 SeqArray_1.30.0    gdsfmt_1.26.0                                                                                                                                 
                                                                                                                                                                                                            
 loaded via a namespace (and not attached):                                                                                                                                                                 
  [1] Rcpp_1.0.5             pillar_1.4.7           compiler_4.0.0                                                                                                                                          
  [4] bigparallelr_0.3.0     GenomeInfoDb_1.26.0    XVector_0.30.0                                                                                                                                          
  [7] bitops_1.0-6           iterators_1.0.13       tools_4.0.0                                                                                                                                             
 [10] zlibbioc_1.36.0        tibble_3.0.4           lifecycle_0.2.0                                                                                                                                         
 [13] nlme_3.1-147           lattice_0.20-41        mgcv_1.8-31                                                                                                                                             
 [16] logistf_1.24           pkgconfig_2.0.3        rlang_0.4.9                                                                                                                                             
 [19] Matrix_1.2-18          foreach_1.5.1          flock_0.7                                                                                                                                               
 [22] parallel_4.0.0         RhpcBLASctl_0.20-137   CompQuadForm_1.4.3                                                                                                                                      
 [25] GenomeInfoDbData_1.2.4 bigassertr_0.1.3       dplyr_1.0.2                                                                                                                                             
 [28] generics_0.1.0         vctrs_0.3.5            Biostrings_2.58.0                                                                                                                                       
 [31] S4Vectors_0.28.0       IRanges_2.24.0         tidyselect_1.1.0                                                                                                                                        
 [34] stats4_4.0.0           grid_4.0.0             data.table_1.13.4                                                                                                                                       
 [37] glue_1.4.2             mice_3.12.0            Biobase_2.50.0                                                                                                                                          
 [40] R6_2.5.0               GWASExactHW_1.01       BiocParallel_1.24.1                                                                                                                                     
 [43] tidyr_1.1.2            purrr_0.3.4            magrittr_2.0.1                                                                                                                                          
 [46] Rsamtools_2.6.0        backports_1.2.0        ellipsis_0.3.1                                                                                                                                          
 [49] codetools_0.2-16       operator.tools_1.6.3   formula.tools_1.7.1                                                                                                                                     
 [52] BiocGenerics_0.36.0    GenomicRanges_1.42.0   splines_4.0.0                                                                                                                                           
 [55] RCurl_1.98-1.2         doParallel_1.0.16      broom_0.7.2                                                                                                                                             
 [58] crayon_1.3.4                         

[gustavahlberg]

Hi Zheng
Will you be addressing this anytime soon?
Just need to know cause otherwise I will make a quick fix myself so I can move on.

Bw,
Gustav

[zhengxwen]

A quick fix could be:

f <- seqOpen("your_gds_file.gds", readonly=F)

node <- index.gdsn(f, "annotation/filter")
(s <- get.attr.gdsn(node)$Description)

put.attr.gdsn(node, "Description", unique(s))

seqClose(f)

[gustavahlberg]

Ah yes. Thank you!

[zhengxwen]

In your case, did you merge multiple gds files with different variants? or multiple gds files with different samples?

[gustavahlberg]

different variants. Actually merging the 200K UKB exome vcfs (gds).

[gustavahlberg]

seqGDS2VCF is also printing "." filter as NA which cause some downstream error since NA is not declared in the header. And I don't know how to rewrite the header in the gds without messing something up.
Also the contigs are converted to 'chrX' -> 'X' (which I prefer) but that is not changed in contigs listed in the header, which also cause some downstream errors.
I tried to fix using write.gdsn() for "description/vcf.contig/ID" but it doesn't work.

[gustavahlberg]

Sorry, solved the last by just using add.gdsn instead of write.gdsn. And I added NA as a filterlevel in filter attribute which seem to work

[zhengxwen]

"seqGDS2VCF is also printing "." filter as NA."
It is fixed in the development version:
http://www.bioconductor.org/packages/devel/bioc/news/SeqArray/NEWS