I ran the following command to extract a subset of regions in my VCF file using tabix:
tabix -h myfile.vcf.gz "11:5247360-5247664" > myfilenew.vcf.gz
For some reason, no matter how I vary my regions, one particular site: 5247358 always comes up in my output. Why is this the case ?
P.S. noob in variant calling and analysing VCF files.
one particular site: 5247358 always comes up in my output
isn't it a variant which is NOT a Single Nucleotide variant ? Is there a END attribute in the INFO column ?...
Just checked it. Yes, there is an END attribute. The END coordinate is overlapping my #POS range.
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Can you show the full VCF line that comes up? Probably has to do with the length of the variant.
Hello and welcome Mehulsharma.253 ,
the quotation marks shouldn't be neccessary. Could you please show the variant(s) that you don't expect? I guess it will be an insdel that overlapt the region you specify.
fin swimmer
BTW:
> myfilenew.vcf.gzwill not create a compressed file. You have to pipe the output oftabixthroughbgzip: