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jpuntomarcos / CNVfilteR

R package to remove false positives of CNV calling tools by using SNV calls
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Incompatible genomes when loading VCF file #9

Closed sunjh22 closed 2 years ago

sunjh22 commented 2 years ago

Hi @jpuntomarcos ,

I am using CNVfilteR to filter false-positive CNVs based on BAF. I successfully loaded CNV region file, but when loading vcf file by loadVCFs(), an error occured: Error in mergeNamedAtomicVectors(genome(x), genome(y), what = c("sequence", : sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY have incompatible genomes: - in 'x': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19 - in 'y': hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38. In the whole process, I used same reference genome from UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/). When loading CNV file, I used genome='hg38'. If I use genome='hg19', another incompatible seqlengths error happened. I also attached a sample vcf file for your reference. sample1.snp.vcf.gz

Do you have any idea of what's happening? Thank you.

jpuntomarcos commented 2 years ago

Hi!

Are you setting genome='hg38' in both loadVCFs() and loadCNVcalls() functions? If so, please, provide me a minimum example that triggers the error so I can check what is happening :)

sunjh22 commented 2 years ago

Hi jpuntomarcos,

Thanks for your reponse, it worked when I also set genome=hg38 in loadVCFs()! Sorry for asking this stupid question... But I suggest also pointing that out in the package manual (I referred to this one: https://bioconductor.org/packages/devel/bioc/vignettes/CNVfilteR/inst/doc/CNVfilteR.html), so everyone knows that genome= is also an option in loadVCFs() function as in loadCNVcalls() function. Have a good day.