Question: extracting Allele Read Counts
0
gravatar for Bogdan
2.5 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 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 • 617 views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Bogdan580
Answer: extracting Allele Read Counts
3
gravatar for James W. MacDonald
2.5 years ago by
United States
James W. MacDonald51k wrote:

Did this answer not suffice? about VCF and BAM files

ADD COMMENTlink written 2.5 years ago by James W. MacDonald51k
Answer: extracting Allele Read Counts
0
gravatar for Bogdan
2.5 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 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 2.5 years ago by Bogdan580
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 2.5 years ago by James W. MacDonald51k

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 2.5 years ago by Bogdan580
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 2.5 years ago by forestylake20

thank you very much !

ADD REPLYlink written 2.5 years ago by Bogdan580
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