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Decipher VCF file similar to 1000 Genomes

Dear All,

I have a VCF file which looks like this :

https://ibb.co/jSnz3J

But , I want to decipher VCF file to look like the below :

https://ibb.co/khCRXd

Please let me know if there is anything I can do to make the file more readable.

Thanks in Advance.

1000 genomes conversion vcf
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updated by zx8754 zx8754 • written by aadhirareddy1323 • aadhirareddy1323

1 answer

use bcftools annotate -x '...' to remove some INFO/FORMAT field https://samtools.github.io/bcftools/bcftools.html

Please let me know if there is anything I can do to make the file more readable.

I wrote : http://lindenb.github.io/jvarkit/VcfToTable.html

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you Pierre for your reply. I get this error "package javax.annotation is declared in module java.xml.ws.annotation, which is not in the module graph" while downloading vcf2table.

• 1 views • link
written by aadhirareddy1323 • aadhirareddy1323

you're using the wrong version of java. Read the manual carefully.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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