Shearwater missing variant
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@darioberaldi-6991
Last seen 2.0 years ago
United Kingdom

Hello,

I'm using Shearwater in the deepSNV package to detect variants. I'm trying to understand why some variants are missed even they seem quite clear from manual inspection. Here's a VCF record as an example:

chr18   5041382 .   A   C   1   PASS    ER=0.142;PI=0.5;AF=0.5;LEN=1    GT:GQ:BF:VF:FW:BW:FD:BD 1:6:0.318:0.21:7:10:40:41   0:3:1:0:0:0:23:15

In the first sample, there are 7+10 reads supporting a variant out of 40+41 reads. This should be a clear variant, however, the Bayes factor is quite high: BF=0.318 and this position would be missed with a sensible cutoff on BF (the default is 0.05).

This is a screenshot of the reads supporting the  variant https://i.imgur.com/1ArCLxt.png

 

And this is the code I used:

library(deepSNV)
bams<- c('286a.bam', '286b.bam')
regions<- makeGRangesFromDataFrame(data.frame(V1= 'chr18', V2=5041250, V3=5041514), seqnames.field= 'V1', start.field= 'V2', end.field= 'V3')
counts<- loadAllData(bams, regions, q= 0)
bf<- bbb(counts)
vcf<- bf2Vcf(bf, counts, regions, samples= bams, cutoff= 0.5)
writeVcf(vcf, 'test.sw.vcf')
# quit R
grep 5041382​ test.sw.vcf

The test data can be found here https://www.dropbox.com/s/vvvmivs7cxp23xt/sw.tar?dl=0 

Am I missing something?

 

sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS release 6.9 (Final)


Matrix products: default

BLAS: /home/db291g/local/lib64/R/lib/libRblas.so

LAPACK: /home/db291g/local/lib64/R/lib/libRlapack.so


locale:

[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       


attached base packages:

[1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

[1] deepSNV_1.22.0             VariantAnnotation_1.22.3   Rsamtools_1.28.0           VGAM_1.0-4                 Biostrings_2.44.1          XVector_0.16.0             SummarizedExperiment_1.6.3 DelayedArray_0.2.7         matrixStats_0.52.2        

[10] Biobase_2.36.2             GenomicRanges_1.28.4       GenomeInfoDb_1.12.2        IRanges_2.10.2             S4Vectors_0.14.3           BiocGenerics_0.22.0        Rhtslib_1.8.0             


loaded via a namespace (and not attached):

[1] Rcpp_0.12.13             compiler_3.4.2           GenomicFeatures_1.28.4   bitops_1.0-6             tools_3.4.2              zlibbioc_1.22.0          biomaRt_2.32.1           digest_0.6.12            bit_1.1-12              

[10] BSgenome_1.44.0          RSQLite_2.0              memoise_1.1.0            tibble_1.3.4             lattice_0.20-35          rlang_0.1.4              Matrix_1.2-11            DBI_0.7                  GenomeInfoDbData_0.99.0

[19] rtracklayer_1.36.4       bit64_0.9-7              grid_3.4.2               AnnotationDbi_1.38.1     XML_3.98-1.9             BiocParallel_1.10.1      blob_1.1.0               GenomicAlignments_1.12.1 colorspace_1.3-2        

[28] RCurl_1.95-4.8   
deepsnv shearwater variant • 1.0k views
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