intersectBed of a a-VCF against a b-GFF

[remi.to...@gmail.com]

Dear list,

I would like to extract SNPs from a VCF file which are localized in CDS. The CDS positions are specified in an external GFF3 file. I considered using intersectBed to perform this step. However, using the command below, the same SNPs can be repeated multiple times. Yet, when I use the -u option, there is no duplicates in the output VCF anymore... but I do not clearly see why intersectBed behaves this way without the -u option since there is no strict "interval" in my VCF, only variant monobase positions.

bedtools intersect \
    -a input.vcf \
    -b cc.gff3 \
    -header > CDS.vcf

Could you explain as to why intersectBed would output redundant SNPs when using the basic intersection method described in the command above?

Thank you very much for your lights,

Sincerely,

Rémi

[Aaron Quinlan]

Hi Remi,

Sorry for the delay.  I suspect this reflects the fact that many SNPs in your VCF intersect multiple transcripts for the same gene(s) in your GTF file. Are you sure that this is not the case?

Best,

Aaron

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[Rémi Tournebize]

Hello Aaron,

Thank you very much for your answer. You are right indeed, I just forgot that there were multiple overlaps in the GFF since it gives intervals for genes/exons/polypeptides, etc. So there is some hierarchical embedding causing SNPs to be called multiple times if I don't use the -u option.

Sorry for this naive question,

Best,

Rémi

[Aaron Quinlan]

Not at all, I am glad it makes sense.

Best,

Aaron

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