Question: How To Convert An Asn.1 Flatfile To A Vcf File That May Be Used In Gatk
gravatar for skm770
7.2 years ago by
skm77010 wrote:

Hi I have to do variant analysis for my Soybean data using GATK. But it requires variant file in VCF format ( especially the BaseRecalibrator step). There is a SNP file available for Soybean at dbSNP but it is in ASN.1 flat file format ( I need to convert the ASN.1 file into VCF

I have tried to look for converters for the same as there has been a mention about them on biostars before: dbsnp file needed for bacteria ) . There are some resources that I have found during my search that seem to say/or do what I want but don't work with ASN.1 format file that I have ( , .

Neither SAMtool's vcfutils nor GATK's VariantsToVCF works in handling ASN.1 file. I would greatly appreciate if someone could guide me to any available software/code that can help me in converting the ASN.1 file to vcf format for use in GATK. Thanks..

gatk next-gen variant • 2.8k views
ADD COMMENTlink modified 5.3 years ago by Biostar ♦♦ 20 • written 7.2 years ago by skm77010
gravatar for Pierre Lindenbaum
7.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

use XML instead of ASN1 :

Transform the XML to VCF using XSLT: An example transforming dbsnp to RDF here:

UPDATE: you cannot convert any rs# to VCF for because none has been mapped to any genetic map. The only content in the ftp directory is:

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Pierre Lindenbaum127k

File generated by the above program does not works with GATK.

ADD REPLYlink written 7.2 years ago by skm770150
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