Hey again,

I experimented a little using scanVcf as import-function for ".bcf files",
but unfortunately it did not work as well as I hoped. Actually not sure if
scanVcf is meant to be used on .bcf files...

#took out ex2.vcf that is the example file in the
VariantAnnotation-package. Processed it as follows:
> asBcf("ex2.vcf",c("20"),"~/Desktop/ex2",overwrite=TRUE)
> b <- scanBcf("ex2.bcf")
Error: scanBcf: failed to find fmt encoded as '18513'
  path: ex2.bcf
#which gives an error similar to yours
#then tried
s <- scanVcf("ex2.bcf")
#No error!
#but the output is to me not really meaningful

#My guess is that your bcf file is corrupt in some way. Possibly because
you used the asBcf() function.
#If you instead use 'Bcftools' for this, the code below is something I know
works (important to use same reference as was used when mapping):
samtools mpileup -ugSf ../References/Bowtie2Hg19/hg19.fa -r chr1
 AllSamples/*.bam | bcftools view -bvcg - > samples-chr1.bcf

#Alternatively you can use readVcf on the original .vcf file and then
create the ASEset-object like this:
VCF <- readVcf("pathToFile")
gr <-  rowData(VCF)
countList <- getAlleleCount(reads, gr, verbose=FALSE)
a <- ASEsetFromCountList(rowData = gr, countList)

/J.R.


On Tue, Jan 14, 2014 at 1:24 PM, Jesper Robert Gadin <j.r.gadin@gmail.com>wrote:

> Hi Tim,
>
> Glad to hear you find the package useful also for validation!
>
> 1) There is no implementation of scanVcf, because I didn't want the
> package to depend on too many other packages. Didn't have problems with the
> scanBcf myself, and therefore saw no reason to include scanVcf. That was
> the reason, but of course I can add an scanVcf option in the import-method!
>
> 2)  Did you mean that the default argument for searchArea could include
> all the ranges in the provided bcf/vcf-file? If so I agree; will include
> that asap.
>
> Expect the new features before next week.
>
> /J.R.
>
>
> On Mon, Jan 13, 2014 at 8:21 PM, Tim Triche, Jr. <tim.triche@usc.edu>wrote:
>
>> Hi all,
>>
>> I'm looking to verify some RNAseq results using (in some cases phased)
>> SNP calls from the CEU trio and from primary samples in-house (case and
>> matched control).  AllelicImbalance looks like a terrific library for this,
>> however my BCFs can't be read by Rsamtools::scanBcf.  (I get an error
>> "Error: scanBcf: failed to find fmt encoded as '16977'  path:
>> /scratch/BAMs/LIU1675A8.hg19.bcf")
>>
>> VariantAnnotation::scanVcf, on the other hand, works fine.
>>
>> So, is there any particular reason why I couldn't hack up
>> the impBcfGL/impBcfGRL method to use VCFs?  Also, would it make sense to
>> have a default argument for searchArea that falls back to the assembly in
>> the metadata, if one is specified?
>>
>> The bizarre thing with the BCFs is that I can scan their headers just
>> fine... !
>>
>> Thanks,
>>
>> Timothy J. Triche, Jr., PhD
>> Jane Anne Nohl Division of Hematology
>> USC/Norris Comprehensive Cancer Center
>>
>
>

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