How To Convert An Asn.1 Flatfile To A Vcf File That May Be Used In Gatk

Question

[skm770]

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 (ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/soybean_3847/). 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 (http://statsandgenomes.wordpress.com/2011/11/06/a-python-script-to-make-a-dbsnp-vcf-file/ , http://svn.mi.fu-berlin.de/seqan/releases/seqan-1.3.1/lib/samtools/bcftools/vcfutils.pl) .

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..

Answer 1

[Pierre Lindenbaum]

use XML instead of ASN1 : ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/soybean_3847/XML/

Transform the XML to VCF using XSLT: An example transforming dbsnp to RDF here: http://plindenbaum.blogspot.fr/2010/02/processing-large-xml-documents-with.html http://lindenb.googlecode.com/svn/trunk/src/xsl/dbsnp2rdf.xsl

UPDATE: you cannot convert any rs# to VCF for ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/soybean_3847/XML/ because none has been mapped to any genetic map. The only content in the ftp directory is:

ds_bin_chNotOn.bin.gz

[skm770]

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