sql to vcf

Question

[fmail1221]

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.

[finswimmer]

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

[fmail1221]

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

[Pierre Lindenbaum]

what is the database engine ? what is the structure of the table ? what is 'Zygosity' ? How To Ask Good Questions On Technical And Scientific Forums

[fmail1221]

• 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)

[swanthana.r]

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.

[Pierre Lindenbaum]

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

bcftools query

[swanthana.r]

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.