I'm having some trouble importing VCFs into seqCAT. I used Sarek to produce VCFs with haplotypecaller and mutect2, and annotated with snpEff and VEP, but importing either fails:

> vcf <-("../VCFs/haplotypecaller/haplotypecaller_T0_CTL_CTL_rep1_snpEff_VEP.ann.vcf.gz")
> create_profile(vcf, 'T0_CTL_CTL_rep1', 'T0_CTL_CTL_rep1.txt')

Reading VCF file ...
Creating SNV profile ...
Error in `[<-.data.frame`(`*tmp*`, !grepl("^rs[0-9]+", data$rsID), "rsID",  :
  replacement has 1 row, data has 0
In addition: Warning messages:
1: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
2: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
3: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames

I've tried the same with tumor-normal VCFs generated with mutect2, but get a different error:

> vcfm<-('../VCFs/mutect/mutect2_T2_CTL_CTL_rep1_vs_T0_CTL_CTL_rep1_snpEff_VEP.ann.vcf.gz')
> create_profile(vcfm, 'T2_CTL_CTL_rep1', 'T2_CTL_CTL_rep1.txt')
Reading VCF file ...
Creating SNV profile ...
Error in `[<-.data.frame`(`*tmp*`, !grepl("^rs[0-9]+", data$rsID), "rsID",  :
  replacement has 1 row, data has 0

I've checked the sample names correspond using VariantAnnotation::scanVcfHeader, but no luck. Any other suggestions?

The two VCFs are here: https://drive.google.com/open?id=1wj68DQkneLzTP65j8u1Y_tsWy7Sn94BM

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] seqCAT_1.4.0                VariantAnnotation_1.28.3    Rsamtools_1.34.0           
 [4] Biostrings_2.50.1           XVector_0.22.0              SummarizedExperiment_1.12.0
 [7] DelayedArray_0.8.0          BiocParallel_1.16.2         matrixStats_0.54.0         
[10] Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.1        
[13] IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] progress_1.2.0           tidyselect_0.2.5         purrr_0.2.5             
 [4] lattice_0.20-35          rtracklayer_1.42.1       GenomicFeatures_1.34.1  
 [7] blob_1.1.1               XML_3.98-1.16            rlang_0.3.0.1           
[10] pillar_1.3.0             glue_1.3.0               DBI_1.0.0               
[13] bit64_0.9-7              bindrcpp_0.2.2           GenomeInfoDbData_1.2.0  
[16] bindr_0.1.1              stringr_1.3.1            zlibbioc_1.28.0         
[19] memoise_1.1.0            biomaRt_2.38.0           AnnotationDbi_1.44.0    
[22] Rcpp_1.0.0               BSgenome_1.50.0          BiocManager_1.30.4      
[25] bit_1.1-14               hms_0.4.2                digest_0.6.18           
[28] stringi_1.2.4            dplyr_0.7.8              grid_3.5.1              
[31] tools_3.5.1              bitops_1.0-6             magrittr_1.5            
[34] RCurl_1.95-4.11          RSQLite_2.1.1            tibble_1.4.2            
[37] tidyr_0.8.2              crayon_1.3.4             pkgconfig_2.0.2         
[40] Matrix_1.2-14            prettyunits_1.0.2        assertthat_0.2.0        
[43] httr_1.3.1               rstudioapi_0.8           R6_2.3.0                
[46] GenomicAlignments_1.18.0 compiler_3.5.1

The first problem is that your `FILTER` column from the variant calling is empty (`.`), as James already pointed out. I have already added a parameter to optionally skip filtering on the `FILTER` column, and I'll likely be adding some kind of check to see if the `FILTER` column is empty, as in your case; these updates will be available in the next devel version, likely within the next week. I'll post here again as soon as I've finished the coding, so you can get back to analysing your data.

The second problem (your comment to James' answer) is also related to your VCF and how the depth is stored in it. By manually inspecting the first VCF (from HaplotypeCaller) you can see that it contains the depth (`DP`) information in the `FORMAT` column: it looks like this: `GT:AD:DP:GQ:PL`. Your second VCF (from mutect) does not follow this procedure, however, and the `DP` information is missing: `GT:AD:AF:F1R2:F2R1:[...]`. As seqCAT works using the data stored in the per-sample column based on the `FORMAT` column and the VariantAnnotation package, the result is that you depth for all variants becomes `NA`.

I have not used mutect myself, so I do not know why it doesn't store the depth information where it is usually stored with other variant callers. I shall look into this and see if I can do something about this. In the meantime, I'll do my best to incorporate the optional filtering code to the devel-version on GitHub (https://github.com/fasterius/seqCAT) as soon as possible, and you should be able to use your original HaplotypeCaller-VCFs.

The FILTER column in (at least the VCF I looked at) are all missing, and create_profile filters on those that are 'PASS', so after that filtering step you have no remaining data. You probably need to figure out how to get Sarek to put something useful in the FILTER column of your VCF.