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locus or gene name in my snps.vcf file

abrahamlovacabrahamlovac Perpignan France Member
edited June 2016 in Ask the GATK team

Hello sorry to trouble you, but I am working with Arabidopsis and In my final file result using GATK I have this information from snps in my sample:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PA01

1 32210 0 T C 13.22 LowQual AC=1 AF=1.00 AN=1 BaseQRankSum=-0.389 ClippingRankSum=0.000 DP=11 FS=7.404 MLEAC=1 MLEAF=1.00 MQ=60.00 MQRankSum=0.000 QD=1.20 ReadPosRankSum=-0.275 SOR=3.352 GT:AD:DP:GQ:PL 1:5 6:11:43:43 0

How I can get the information of gene description or localization from those snps? (For example AT5G28540)

Thanks in advance

Abraham

Best Answer

Answers

  • abrahamlovacabrahamlovac Perpignan France Member

    Thank you Geraldine, another question is Do you know if for Arabidopsis is there a dbSNP.vcf file, So I can used as [--dbsnp dbSNP.vcf]:

    java -jar GenomeAnalysisTK.jar \
    -R reference.fasta \
    -T HaplotypeCaller \
    -I sample1.bam [-I sample2.bam ...] \
    [--dbsnp dbSNP.vcf] \
    [-stand_call_conf 30] \
    [-stand_emit_conf 10] \
    [-L targets.interval_list] \
    -o output.raw.snps.indels.vcf

    Thanks in advance

  • abrahamlovacabrahamlovac Perpignan France Member

    Thank you Geraldine, another question is Do you know if for Arabidopsis is there a dbSNP.vcf file, So I can used as [--dbsnp dbSNP.vcf]:

    java -jar GenomeAnalysisTK.jar \
    -R reference.fasta \
    -T HaplotypeCaller \
    -I sample1.bam [-I sample2.bam ...] \
    [--dbsnp dbSNP.vcf] \
    [-stand_call_conf 30] \
    [-stand_emit_conf 10] \
    [-L targets.interval_list] \
    -o output.raw.snps.indels.vcf

    Thanks in advance

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    I expect there is one since it is a model organism, but I've never worked with it myself so I don't know where you can find it.
  • abrahamlovacabrahamlovac Perpignan France Member

    Thanks, you are very kind. I resolve my problem using SnpEff, as you suggest me

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