Filter track list and variant list

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2.1 years ago

Cong-Phuoc • 0

I have two list, first list contains defined variants (200 variants) and the second list is actually a .vcf file which contains all variants of 1000 samples. I want to check whether my 1000 samples contains one or some variants in my first list or not. Something like VLookUp in excel Could you please tell me how to do that? I am trying to use IGV to open the .vcf file, but I cannot found a way to filter like above

Thanks

sample list filters variant • 550 views

ADD COMMENT • link updated 2.1 years ago by brunobsouzaa ▴ 830 • written 2.1 years ago by Cong-Phuoc • 0

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First, you don't use IGV to open .vcf files. For that, you have to specify the genomic coordinates you want to check, after loading the bam file on it. For comparing your list against your .vcf file, check bcftools. It will do what you need!

ADD REPLY • link 2.1 years ago by brunobsouzaa ▴ 830

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Select a subset of variants from a larger vcf file

ADD REPLY • link 2.1 years ago by zx8754 11k

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