Hello Valerie,

I am running VariantAnnotation package to locate the position of SNPs using
locateVariants.

The commands that I gave to extract vcf file and the gff file are as
follows:

###Reading the vcf file
vcf1<-readVcf("CGTACG_filteredSNPS.vcf","Pinfestans.fa")
rd<-rowData(vcf1)

####imported and converted the gff3 file to GRangesList object
subject<-import.gff("annotation.gff3")
myGRanges<-as(subject,"GRanges")
myGRangesList<-GRangesList(myGRanges)


### made sure that both of them have same sequence levels
rd<-keepSeqlevels(rd,intersect(seqlevels(rd),seqlevels(myGRangesList))
myGRangesList<-keepSeqlevels(myGRangesList,intersect(seqlevels(rd),seqlevels(myGRangesList))

###Ran the locateVariants command
variants_found<-locateVariants(rd,myGRangesList,CodingVariants())

###Got the following error
Error in DataFrame(...) : different row counts implied by arguments

Can you please point to what I am doing wrong?

Regards
Jolly


-- 
Jolly Shrivastava
Ph.D candidate (Genetics, Genomics and Bioinformatics)
University of California, Riverside

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