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Question: extracting Allele Read Counts
0
gravatar for Bogdan
22 months ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

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

rsamtools vcf • 494 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by Bogdan550
Answer: extracting Allele Read Counts
3
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald49k wrote:

Did this answer not suffice? about VCF and BAM files

ADD COMMENTlink written 22 months ago by James W. MacDonald49k
Answer: extracting Allele Read Counts
0
gravatar for Bogdan
22 months ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

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           

ADD COMMENTlink written 22 months ago by Bogdan550
1

You have been around for 9 years now. Is it fair if I yell at you for using the Add your answer box to add an additional question?

Also, you have some outdated packages. You need to run biocLite to first make sure you have the latest versions before looking for suggestions. Also, giving the results of traceback right after the error would be helpful.

ADD REPLYlink written 22 months ago by James W. MacDonald49k

Thank you James for suggestions ... if you were in Palo Alto, I would have invited you for a lunch (and beer ? ;) Sometimes, I am in rush -- just too many things to do. Thanks again for advice : will do accordingly. 

ADD REPLYlink written 22 months ago by Bogdan550
1

I've experienced this error recently as well...here you go A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) I just followed the advice here and re-installed the affected packages using type="source". 

 

ADD REPLYlink written 22 months ago by forestylake20

thank you very much !

ADD REPLYlink written 22 months ago by Bogdan550
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