SelectVariants quick question about concordance/discordance

myoglumyoglu Posts: 39Member
edited November 2013 in Ask the GATK team

This is my code:

java -Xmx4g -jar GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar \
    -R genome.fa \
    --filter_reads_with_N_cigar \
    -T CombineVariants \
    -V:NORMALSpost RNA-edit_SNPs_NORMALS-post_SNPeff_VA.vfc \
    -V:OMNI 1000G_omni2.5.hg19.vcf \
    -V:db137 dbsnp_137.hg19.vcf \
    -V:Hapmap hapmap_3.3.hg19.vcf \
    -V:ESP1,VCF ESP6500SI-V2-SSA137.updatedRsIds.Allchr.snps_indels_FIX.vcf \
    --out NORMALS-post_TruePositives_raw.vcf &&

java -Xmx4g -jar GenomeAnalysisTK.jar \
    -R genome.fa \
    --filter_reads_with_N_cigar \
    -T SelectVariants \
    -V NORMALS-post_TruePositives_raw.vcf \
    -select "set == 'NORMALSpost'" \
    --out NORMALS-post_TruePositives.vcf

I hope I got this right: I now have SNPs (I have only called SNPs, not indels) that is found in my sample, 1000G, dbSNP and ESP. Right?

Can I easily make a VCF with all SNPs in MY sample only, not found in anything else by tweaking this code? Or must I do it some way else?


Post edited by Geraldine_VdAuwera on

Best Answer


  • myoglumyoglu Posts: 39Member

    If there is not I have an alternative strategy:

    Using CombineVariants to "merge" all my references (1000g etc)

    Use SelectVariants discordance option against this "merged" vcf

  • myoglumyoglu Posts: 39Member

    Yes, thats what I finally did. Thanks!

  • n_mahfouzn_mahfouz GermanyPosts: 3Member

    Hi Geraldine,
    I would like to get variants unique to a data set as well, but i was wondering if i could compare against reads rather than other variants ... is there an alternative that applies to my problem??

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,438Administrator, GATK Dev admin

    @n_mahfouz If I'm not mistaken, you also posted this same question as a new thread, right? Please don't do that; we read and respond to everything, so double postings make us waste time.

    Geraldine Van der Auwera, PhD

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