The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

SelectVariants quick question about concordance/discordance

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

Hi!
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?

Question:
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?

Thanks!

Post edited by Geraldine_VdAuwera on

Best Answer

Answers

  • myoglumyoglu Posts: 39

    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: 39

    Yes, thats what I finally did. Thanks!

  • n_mahfouzn_mahfouz GermanyPosts: 3

    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??
    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 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

Sign In or Register to comment.