Dear all,

please could you advise : given a (tumor) BAM file and a (germline) VCF file, what tool shall i use in order to extract the Allele Read Counts for each heterozygous SNP (from the vcf file) ? Many thanks, 

-- bogdan

Did this answer not suffice? about VCF and BAM files

Dear James, thank you for reminding me. I am encountering an issue though (below): any suggestions on how to fix it it would be fabulous. Thanks a lot ;) The vcf file looks OK to me. 

 x<-VariantAnnotation::readVcf("germline.HETERO.chr19.vcf", genome="hg38")
Error in c(DataFrameList(META = meta), tbls[unique(tags)]) :
  could not find symbol "recursive" in environment of the generic function
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
 [1] VariantAnnotation_1.20.2   SummarizedExperiment_1.4.0
 [3] Biobase_2.34.0             Rsamtools_1.26.1          
 [5] Biostrings_2.42.1          XVector_0.14.0            
 [7] GenomicRanges_1.26.2       GenomeInfoDb_1.10.2       
 [9] IRanges_2.8.1              S4Vectors_0.12.1          
[11] BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9              AnnotationDbi_1.36.2     GenomicAlignments_1.10.0
 [4] zlibbioc_1.20.0          BiocParallel_1.8.1       BSgenome_1.42.0         
 [7] lattice_0.20-34          tools_3.3.3              grid_3.3.3              
[10] DBI_0.5-1                digest_0.6.12            Matrix_1.2-8            
[13] rtracklayer_1.34.1       bitops_1.0-6             biomaRt_2.30.0          
[16] RCurl_1.95-4.8           memoise_1.0.0            RSQLite_1.1-2           
[19] GenomicFeatures_1.26.2   XML_3.98-1.5