separate meta-population data from VCF

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2.7 years ago

paolobareng • 0

Hi everyone,

I have a meta-population data in vcf file. Is there a way to separate them according to their population/country and the outcome would be countryname.vcf?

Thanks, Paolo

vcf • 694 views

ADD COMMENT • link updated 2.7 years ago by iraun 6.2k • written 2.7 years ago by paolobareng • 0

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Can you provide an example of the VCF?

ADD REPLY • link 2.7 years ago by iraun 6.2k

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Hi Iraun -- Here's an example of my vcf. I'm trying to separate VCF based on their countries (Brazil, Colombia, etc):

fileformat=

fileDate=

source=

ALT=<ID=NON_REF,Description=

contig=<ID=CHR1,length=1021664>

INFO=<ID=AC,Number=A,Type=Integer,Description="

FILTER=<ID=PASS,Description="All filters passed">

FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

GATKCommandLine=""

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Brazil01 Colombia01 ...

CHR1 1459366 . A G 634.58 PASS

ADD REPLY • link 2.7 years ago by paolobareng • 0

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Maybe you can use any of the solutions suggested in Individual VCF files from main VCF file?

ADD REPLY • link 2.7 years ago by iraun 6.2k

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