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sql to vcf

Hi all I'm trying to convert sql data containing headers such as 'CHROM' 'POS' 'REF' 'ALT' 'Zygosity' to the variant call format (vcf) file. Can anybody help me? My operating system is windows 10.

database sql vcf
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updated by swanthana.r 1 • | written by fmail1221 0
  • I'm trying to convert sql data to the vcf file.
  • Database engine=DBMS : MS SQL (2017) on Windows 10 Schema:dbo
  • Structure of the table=My data in TABLE: String, Int, fload
  • Zygosity=a colum that is containing HET (hetrozygote) or HOM (homozygote)
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updated by finswimmer 1.6K • | written by fmail1221 0

Hello fmail1221 ,

and what is your problem? Have a look at the specification on how a vcf must look like and extract the data from your database to make a valid vcf.

fin swimmer

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written by finswimmer 1.6K

Hello finswimmer, I want a converter to convert my data from sql server to the vcf file.

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written by fmail1221 0

Did you get the vcf file format from database. I am trying to get output vcf file from psql database.

Or Are there any tools to convert tab delimited file to vcf file. I have a file with CHROM, POS, REF and ALT, can we use any tool to convert it into vcf file. Let me know. Thank you.

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written by swanthana.r 1

Are there any tools to convert tab delimited file to vcf file.

bcftools query

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written by Pierre Lindenbaum 17K

Pierre, Thanks for quick reply.

bcftools query can extract tab delimited file from vcf/bcf format right, but I need a vcf file from tab delimited file. I found the below lines from bcftools document page.

bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]] Extracts fields from VCF or BCF files and outputs them in user-defined format.

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written by swanthana.r 1

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