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Weird VQSR filtering pattern


I performed HC joint calling against 300 normal tissue samples. I did every step according to the best practice and got a VQSR plot very similar to this one. Most variants have the same MQ and FS value and make these feature distribution non-gaussian. Would such result be still valid? Can anyone share some insight?



  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @UniCorn

    Please post the version of GATK you are using, the exact command and the plots showing the weird VQSR filtering pattern.

  • UniCornUniCorn USMember

    The version is GATK4.0.8.1

    command line is :
    /biocluster/data/bioexec/software/gatk- VariantRecalibrator \
    -R $REF \
    -V $input_vcf \
    -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 \
    -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 \
    --resource hapmap,known=false,training=true,truth=true,prior=15.0:$ref_dir/hapmap_3.3.hg19.sites.vcf \
    --resource omni,known=false,training=true,truth=false,prior=12.0:$ref_dir/1000G_omni2.5.hg19.sites.vcf \
    --resource dbsnp,known=true,training=false,truth=false,prior=2.0:$dbsnp_vcf \
    -an MQRankSum -an ReadPosRankSum -an BaseQRankSum -an SOR -an MQ -an FS -an DQ \
    -mode SNP \
    -O $outdir/$output_prefix.snp.recal \
    --tranches-file $outdir/$output_prefix.snp.tranches \
    --rscript-file $outdir/$output_prefix.snp.plots.R

    I guess the reason is that MQ, FS and DQ does not follow Gaussian distribution (shows as very sharp peak with little standard deviation). Should I get ride of these non-Gaussian features? Is there a role of thrum regarding which features should be included? Thanks

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @UniCorn

    Can you also please post the VQSR plots that are showing the weird results.

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