I'm getting the same error message as found in this post when running the create_profile function from seqCAT:

> create_profile(vcf, "SRR7789342", "SRR7789342_profile.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
4: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrM, chr15_KI270727v1_random, chrY_KI270740v1_random, chrUn_KI270304v1, chrUn_KI270305v1, chrUn_KI270322v1, chrUn_KI270320v1, chrUn_KI270312v1, chrUn_KI270412v1, chrUn_KI270419v1, chrUn_KI270420v1, chrUn_KI270424v1, chrUn_KI270417v1, chrUn_KI270422v1, chrUn_KI270425v1, chrUn_KI270528v1, chrUn_KI270539v1, chrUn_KI270548v1, chrUn_KI270334v1, chrUn_KI270335v1, chrUn_KI270338v1, chrUn_KI270340v1, chrUn_KI270336v1, chrUn_KI270364v1, chrUn_KI270366v1, chrUn_KI270379v1, chrUn_KI270389v1, chrUn_KI270395v1, chrUn_KI270388v1, chrUn_KI270386v1, chrUn_KI270376v1, chrUn_KI270374v1, chrUn_KI270372v1, chrUn_KI270373v1, chrUn_KI270375v1, chrUn_KI270371v1, chrUn_KI270752v1, chrUn_KI270755v1, chr1_KI270762v1_alt, chr1_KI270766v1_alt, chr1_KI270760v1_alt, chr1_GL383518v1_alt, chr1_KI270761v1_alt, chr2_KI270770v1_alt, chr2_KI270773v1_alt, chr2_KI270775v1_alt, chr2_KI270771v1_alt, chr2_KI270776v1_alt, chr2_KI270767v1_alt, chr [... truncated]

It looks like all of my variants are being filtered out? I double-checked the source code for the create_profile function, and I understand that the following filters exist: 1. Remove variants without "PASS" in the FILTER column. 2. Remove variants with depth below default of 10. 3. Remove non-variants, i.e. any row with greater than one char in the REF or ALT columns.

I went back to my .vcf to inspect for these filters, and I found a row that passes all those criteria:

chr1    187485  .       G       A       855.6   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-0.656;DP=37;ExcessHet=3.0103;FS=2.005;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=23.12;ReadPosRankSum=2.135;SOR=0.283;ANN=A|synonymous_variant|LOW|FO538757.1|ENSG00000279457|transcript|ENST00000623083.3|protein_coding|7/11|c.771C>T|p.Asn257Asn|771/1687|771/1395|257/464||,A|synonymous_variant|LOW|FO538757.1|ENSG00000279457|transcript|ENST00000623834.3|protein_coding|8/10|c.768C>T|p.Asn256Asn|768/1374|768/1080|256/359||,A|synonymous_variant|LOW|FO538757.1|ENSG00000279457|transcript|ENST00000624735.1|protein_coding|9/15|c.804C>T|p.Asn268Asn|1040/1604|804/1368|268/455||,A|downstream_gene_variant|MODIFIER|FO538757.2|ENSG00000279928|transcript|ENST00000624431.1|protein_coding||c.*3327G>A|||||3327|,A|downstream_gene_variant|MODIFIER|MIR6859-2|ENSG00000273874|transcript|ENST00000612080.1|miRNA||n.*406C>T|||||406|  GT:AD:DP:GQ:PL  0/1:5,32:37:62:863,0,62

So, why would this row be filtered out? I know that create_profile calls filter_annotations to filter for the highest impact variants. Is this row getting filtered out because its impact in marked as LOW?

For reference, I used HaplotypeCaller, VariantFiltration and snpEff to get the final .vcf here: https://drive.google.com/open?id=1vfih6-QWPuczqHYDRhx6ygzzD8EjeRDm.

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

other attached packages:
 [1] seqCAT_1.4.1                VariantAnnotation_1.27.9
 [3] Rsamtools_1.33.7            Biostrings_2.49.2
 [5] XVector_0.21.4              SummarizedExperiment_1.11.6
 [7] DelayedArray_0.7.48         BiocParallel_1.15.15
 [9] matrixStats_0.54.0          Biobase_2.41.2
[11] GenomicRanges_1.33.14       GenomeInfoDb_1.17.4
[13] IRanges_2.15.18             S4Vectors_0.19.22
[15] BiocGenerics_0.27.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0               lattice_0.20-35          prettyunits_1.0.2
 [4] ps_1.2.0                 assertthat_0.2.0         rprojroot_1.3-2
 [7] digest_0.6.18            R6_2.3.0                 backports_1.1.2
[10] RSQLite_2.1.1            httr_1.3.1               zlibbioc_1.27.0
[13] rlang_0.3.0.1            GenomicFeatures_1.33.4   progress_1.2.0
[16] curl_3.2                 callr_3.0.0              blob_1.1.1
[19] Matrix_1.2-14            desc_1.2.0               devtools_2.0.1
[22] stringr_1.3.1            RCurl_1.95-4.11          bit_1.1-14
[25] biomaRt_2.37.9           munsell_0.5.0            compiler_3.5.1
[28] rtracklayer_1.41.8       pkgconfig_2.0.2          base64enc_0.1-3
[31] pkgbuild_1.0.2           GenomeInfoDbData_1.2.0   XML_3.98-1.16
[34] crayon_1.3.4             withr_2.1.2              GenomicAlignments_1.17.3
[37] bitops_1.0-6             grid_3.5.1               gtable_0.2.0
[40] DBI_1.0.0                magrittr_1.5             cli_1.0.1
[43] stringi_1.2.4            fs_1.2.6                 remotes_2.0.1
[46] testthat_2.0.1           tools_3.5.1              bit64_0.9-7
[49] glue_1.3.0               BSgenome_1.49.5          hms_0.4.2
[52] processx_3.2.0           pkgload_1.0.1            AnnotationDbi_1.44.0
[55] colorspace_1.3-2         BiocManager_1.30.3       sessioninfo_1.1.0
[58] memoise_1.1.0            usethis_1.4.0