[BioC] Extracting variant nucleotides

[Valerie Obenchain]

Michael,

Is globalToQuery similar to globalToLocal in VariantAnnotation? It looks 
like a C implementation of the same idea ...?


Alpesh,

You may also want to check out these functions from the 
VariantAnnotaiton package,
?globalToLocal
?predictCoding


Valerie


On 11/03/2011 11:22 AM, Michael Lawrence wrote:
> There is a function inside GenomicRanges that maps from global positions to
> read positions, considering the cigar. I have not exported it yet, because
> I want the output (the mapping) to have a formal class, like RangesMapping.
> Haven't had time to do that yet. Anyone want to pick it up for me? Also, I
> think we should use a generic for this, perhaps map() that does this when
> given a GRanges (of variants) and a GappedAlignments (reads).
>
> Anyway, it is here:
> GenomicRanges:::globalToQuery.
>
> YMMV.
>
> Michael
>
> On Thu, Nov 3, 2011 at 10:54 AM, Alpesh Querer<alpeshq at gmail.com>  wrote:
>
>> Hi All,
>>
>> I want to know if there is a way to extract variant nucleotide(s) from
>> reads
>> that align to particular locations. This should also take care of the
>> soft/hard clips, split alignments etc.
>> I have a filtered BAM file with reads which cover my loci of interest.  For
>> example an an insertion GAA
>> exists in the reference at ch1:1234-1236. I want to tabulate all variant
>> alleles at ch1:1234-1236.
>>
>> Thanks,
>> Alpesh
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor