I am running a variant calling pipeline to detect solid tumours and haematological alterations. The variant calling is done with Mutect2.
I noticed, however, that the output of the header command (VariantAnnotation library) is not the same considering two versions (1.24.5 vs. 1.32.0).
When using v 1.32.0 I get
> header(input)
class: VCFHeader
samples(1): Panel-STHT-T210986-PJR
meta(6): MutectVersion fileformat ... GATKCommandLine contig
fixed(1): FILTER
info(16): CONTQ DP ... STR TLOD
geno(13): GT AD ... SAAF SAPP
Whereas when using v 1.24.5 I don't get the line fixed(1): FILTER:
> header(input)
class: VCFHeader
samples(1): Panel-STHT-T210986-PJR
meta(3): META GATKCommandLine contig
fixed(0):
info(16): CONTQ DP ... STR TLOD
geno(13): GT AD ... SAAF SAPP
I also noticed that if I continue with the filtering that the R script does (eventually writing a vcf with writeVcf), with VariantAnnotation v 1.32.0 I get an extra line in the vcf header: ##FILTER=All filters passed, which is upsetting another downstream program (the error message that I get is .vcf: Invalid FILTER line). And it appears to me that this ##FILTER=All filters passed line is actually coming from the extra line of the header command.
The easiest solution for me would be to downgrade from 1.32.0 to 1.24.5: However, I would like to understand where this extra line comes from
Session information (when using v1.32.0 of VariantAnnotation is shown below:
R version 3.6.1 (2019-07-05)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 8 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_BE.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=de_BE.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=de_BE.UTF-8 LC_NAME=de_BE.UTF-8
[9] LC_ADDRESS=de_BE.UTF-8 LC_TELEPHONE=de_BE.UTF-8
[11] LC_MEASUREMENT=de_BE.UTF-8 LC_IDENTIFICATION=de_BE.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] httr_1.4.1 stringr_1.4.0
[3] readr_1.3.1 xlsx_0.6.3
[5] VariantAnnotation_1.32.0 Rsamtools_2.2.3
[7] Biostrings_2.54.0 XVector_0.26.0
[9] SummarizedExperiment_1.16.1 DelayedArray_0.12.2
[11] BiocParallel_1.20.1 matrixStats_0.55.0
[13] Biobase_2.46.0 GenomicRanges_1.38.0
[15] GenomeInfoDb_1.22.0 IRanges_2.20.2
[17] S4Vectors_0.24.3 BiocGenerics_0.32.0
[19] optparse_1.6.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 lattice_0.20-38 prettyunits_1.0.2
[4] xlsxjars_0.6.1 assertthat_0.2.1 zeallot_0.1.0
[7] digest_0.6.15 BiocFileCache_1.10.2 R6_2.2.2
[10] backports_1.1.4 RSQLite_2.1.1 pillar_1.4.2
[13] zlibbioc_1.32.0 rlang_0.4.0 GenomicFeatures_1.38.2
[16] progress_1.2.2 curl_4.2 blob_1.1.1
[19] Matrix_1.2-17 RCurl_1.98-1.1 bit_1.1-14
[22] biomaRt_2.42.0 compiler_3.6.1 rtracklayer_1.46.0
[25] pkgconfig_2.0.3 askpass_1.1 openssl_1.4.1
[28] tidyselect_0.2.5 tibble_2.1.3 GenomeInfoDbData_1.2.2
[31] XML_3.98-1.11 crayon_1.3.4 dplyr_0.8.3
[34] dbplyr_1.4.2 GenomicAlignments_1.22.1 bitops_1.0-6
[37] rappdirs_0.3.1 grid_3.6.1 DBI_1.0.0
[40] magrittr_1.5 stringi_1.4.3 getopt_1.20.3
[43] vctrs_0.2.0 tools_3.6.1 bit64_0.9-7
[46] BSgenome_1.54.0 glue_1.3.1 purrr_0.3.2
[49] hms_0.5.1 AnnotationDbi_1.48.0 memoise_1.1.0
[52] rJava_0.9-11
