This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Convert An Asn.1 Flatfile To A Vcf File That May Be Used In Gatk

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..

variant gatk next-gen
• 4,021 views • link
updated by Biostar Biostar • written by skm770 • skm770

1 answer

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
• 23 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

• 173 views • link
written by skm770 • skm770

Log in to answer this question.

More posts like this
  • ClinVar local install
    written by win win
    Hi all. I want to do downstream analysis of VCF files and need to interface my data with ClinVar. I found ClinVar in VCF format …
  • Known SNPs for rice for Base recalibration using GATK
    written by Floydian_slip Floydian_slip
    Hi, I am analyzing rice samples for SNP detection using GATK, and for the base recalibration, I need a set of known sites for rice. …
  • Extracting Information From Vcf File About Heterozygous,Homozygous From Gatk Pipeline And Comparing…
    written by skm770 • skm770
    <p>Hi </p> <p>We have analyzed some data-sets for genome analysis using a couple of different pipelines : <a href='http://bio-bwa.sourceforge.net/'>bwa</a>-GATK, GSNAP-Samtools and for few soybean genomes. …
  • Discrepancy Between Ncbi / Vcf And Ncbi / Html
    written by Pierre Lindenbaum Pierre Lindenbaum
    <p>in the VCF for dbsnp137, <a href='http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=11412589'>rs11412589</a> is said to be located at <strong>chr9:74300311</strong></p> <pre><code>$ curl -s "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz" |gunzip -c | grep BUILD ##dbSNP_BUILD_ID=137 ~$ …
  • Minor Allele Frequency Nucleotide In Dbsnp?
    written by mylons mylons
    <p>I have a vcf of dbsnp-137, and it occasionally has a GMAF info field with an allele frequency. What I don't understand is how to …
  • Split Vcf File Into Snps And Indels
    written by pablo.riesgo • pablo.riesgo
    <p>Hi there,</p> <p>As recommended in the GATK best practices the Variant Quality Score Recalibration has to be done separately for SNPs and Indels. But, I …
  • High-Quality Zebrafish Dbsnp Database
    written by michealsmith michealsmith
    <p>How to download zebrafish dbSNP database, in vcf format at the best?</p> <p>I've checked UCSC: <a href="http://genome.ucsc.edu/cgi-bin/hgTables?org=Zebrafish&amp;db=danRer7&amp;hgsid=255390817&amp;hgta_doMainPage=1)">http://genome.ucsc.edu/cgi-bin/hgTables?org=Zebrafish&amp;db=danRer7&amp;hgsid=255390817&amp;hgta_doMainPage=1)</a> It's werid there's no dbSNP column for fish; …
  • [Errno 8] Exec Format Error Using Tophat 1.3.1
    written by Marina Manrique Marina Manrique
    <p>Hi all,</p> <p>I've installed Tophat 1.3.1 following <a href='http://tophat.cbcb.umd.edu/tutorial.html#inst'>these instructions</a> </p> <p>and when I run the test command to know if the installation has gone …
  • Dbsnp In Vcf Format
    written by Andrea_Bio • Andrea_Bio
    <p>Hello</p> <p>I have seen that dbSNP makes human SNP data available in VCF 4.0 format but not for other organisms. I would like to have …
  • Dbsnp132 1000Genomes Vcf File Info Field: Bitfield Structure
    written by Biomed Biomed
    <p>The new 1000Genomes+dbSNP132 resource (<a href='ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz'>ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz</a>) has dbSNP byte structured information about snps.</p> <p>One such example is VP=050100000a0105051a000100 </p> <p>Considering the information found here <a …