How Can I Get strand Bias Imformation From Mutect?

Hi,
Mutect does have filter for strand bias, but does not give strand imformation(like DP4 or other ) in its output .call file or .vcf file.
But sometimes I wanna check the strand distribution of the SNV called and have further filtering, I wonder how could I get such imformation?

Thanks! Hartblue

Best Answers

Answers

  • hartbluehartblue Member

    @Geraldine_VdAuwera said:
    Hi hartblue,

    You can add strand bias annotation (counts of fwd and rev reads per allele) to your VCF using GATK's VariantAnnotator. You will need to pass in the original BAM file. See the GATK documentation for more details.

    Hi,
    really thanks! I tried to annotate but nothing had been added to the output VCF. lol
    Am I doing things right?Thanks a lot!
    hartblue

    java -Xmx8g -jar GenomeAnalysisTK.jar \
    -R $PATH_REF \
    -T VariantAnnotator \
    -I /public/data/exome/Project_XH/RUN130727/Sample_XHDG39N/XHDG39N.ready.bam \
    -I /public/data/exome/Project_XH/RUN130727/Sample_XHDG39C/XHDG39C.ready.bam \
    -o $outputvcf \
    -A DepthPerAlleleBySample \
    --variant $inputvcf \
    -L $inputvcf \
    --dbsnp $PATH_DBSNP_138

  • hartbluehartblue Member

    @Geraldine_VdAuwera said:
    Well, that's a valid command line but it's for adding the AD annotation, not SB. For SB you need to request StrandBiasBySample. You can request several annotations at the same time of course.

    Sorry, I paste the wrong command. I did tried StrandBiasBySample earlier, however nothing has been annotated(it did add ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> to the header, but no variation has been annotated)

    I find this problem exists for all kinds of "Available annotations for the VCF FORMAT field". Meanwhile, those "Available annotations for the VCF INFO field" works quite fine. Do you have any advice for me? Really appreciate your help!

    Hartblue

  • LindaLinda Member
    Hi,
    Sorry to ask this question again but I am very urgent. I tried to annotate StrandBiasBySample to the vcf file using GATK v3.7 but nothing had been added to the output vcf file. I also met the same question as @hartblue said (I find this problem exists for all kinds of "Available annotations for the VCF FORMAT field". Meanwhile, those "Available annotations for the VCF INFO field" works quite fine.). I can't find any further answer from yours.

    I also tried Haplotypecall v3.7 to add the StrandBiasSample and it works fine. But with the Mutect2 (GATK4), I can't add the information.

    Do you have any ideas for me to add the StrandBiasBySample to the output vcf file of the somatic mutect by VariantAnnotator (GATK 3.7) or Mutect2 (GATK4)?

    Linda
  • manbamanba Member ✭✭

    @Linda, is the F1R2 F2R1that you wanted in gatk4 mutect2

  • LindaLinda Member
    @manda Yes, that is what I need, thanks
  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @Linda did that answer your question or do you need assistance? According to the documentation on [this page] (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_annotator_StrandBiasBySample.php)

    This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator).

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