Re: Best practices to find intersection among variants

Thanks a lot, make sense. So, just to confirm,

o.l <- findOverlaps(vcf1,vcf2)

Where vcf1 and vcf2 are VCF object would not work, it would operate on the
Granges and would consider the alt.

--  Marco Blanchette, Ph.D.
Genomic Scientist
Stowers Institute for Medical Research
1000 East 50th Street
Kansas City MO 64110
www.stowers.org


Tel: 816-926-4071 
Cell: 816-726-8419 
Fax: 816-926-2018





On 8/25/14, 8:01 PM, "Michael Lawrence" <[email protected]> wrote:

>Just to clarify, you'll need to get a VRanges via
>
>vr <- as(vcf, "VRanges")
>
>Michael
>
>
>On Mon, Aug 25, 2014 at 5:13 PM, Julian Gehring <[email protected]>
>wrote:
>
>> Hi Marco,
>>
>> Essentially, you want to find a intersection with both the locus and the
>> ref/alt alleles matching.  The 'VariantAnnotation' has the 'match'
>>function
>> which does this (matching the alt allele).  Here is some of my code for
>> getting the common variants from two 'VRanges' objects:
>>
>>   intersectVRanges <- function(x, y) {
>>       m = match(x, y)
>>       s1 = x[!is.na(m)]
>>       s2 = y[m[!is.na(m)]]
>>       res = list(s1, s2)
>>       return(res)
>>   }
>>
>> Best
>> Julian
>>
>>
>> On 25.08.2014 16:35, Blanchette, Marco wrote:
>>
>>> I am very very new to working with variants, maybe this question is
>>>very
>>> basic but I need to get kickstarted a bit�
>>>
>>> Just ran an analysis to find the common variation in a set of lab
>>>strains
>>> used in house in the haploid genomes of S. pombe. I used GATK best
>>> practices and I am at the stage where I have filtered variants and I
>>>would
>>> like to find the common ones. My first intuition for this was to turn
>>>to R
>>> (tired to running Java command line�) and I fumbled on
>>>VariantAnnotation
>>> which uses my favorite object, GRanges, under the hood. So I should be
>>>good.
>>>
>>> However, I can�t seem to figure out how to create intersect and I am a
>>> bit nervous as I want to find the common variants, not just the
>>>location (I
>>> can see that I could extract the Granges and do overlap operation on
>>>them,
>>> but then, I run into the danger of losing the variant information�).
>>>
>>> Could anyone provide a simple workflow to get me started? I could
>>>provide
>>> a basic starting code but it would only be restricted to loading the
>>> VariantAnnotation package and reading two vcf files� so I figured that
>>>I
>>> would not add it�
>>>
>>> Thanks a bunch and sorry for the very vcf newby question.
>>>
>>>
>>> --  Marco Blanchette, Ph.D.
>>> Genomic Scientist
>>> Stowers Institute for Medical Research
>>> 1000 East 50th Street
>>> Kansas City MO 64110
>>> www.stowers.org
>>>
>>> Tel: 816-926-4071
>>> Cell: 816-726-8419
>>> Fax: 816-926-2018
>>>
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>>>
>>>
>>>
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