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  • wanguan2000
    Member
    • Nov 2010
    • 24

    #1

    GATK VariantFiltration undefined variable AB

    java -Xmx4g -jar ./GenomeAnalysisTK-1.1-12-g2d94037/GenomeAnalysisTK.jar \
    -l INFO \
    -nt 8 \
    -R ucsc.hg19.fasta \
    -T UnifiedGenotyper \
    -I ./testdata/32bwa_RG_realign_dedup_mate_recal.bam \
    -B:dbsnp,vcf /share/user_data/wfz1/database/hg19database/dbsnp_132.hg19.vcf \
    -o ./testdata/snps.raw32.vcf \
    -stand_call_conf 50.0 \
    -stand_emit_conf 10.0 \
    -dcov 500

    when I got the snps.raw32.vcf like this:
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HGExon31
    chrM 150 . T C 353.47 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=3.154;DP=18;Dels=0.00;FS=13.570;HRun=1;HaplotypeScore=1.8455;MQ=50.58;MQ0=0;MQRankSum=2.169;QD=19.64;ReadPosRankSum=1.971;SB=-129.49 GT:ADP:GQ:PL 0/1:5,13:18:96.57:383,0,97
    ...
    But when I run this:
    java -jar ./GenomeAnalysisTK-1.1-12-g2d94037/GenomeAnalysisTK.jar \
    -T VariantFiltration \
    -R ucsc.hg19.fasta \
    -B:dbsnp,vcf /share/user_data/wfz1/database/hg19database/dbsnp_132.hg19.vcf \
    -o ./testdata/snps.filtered31.vcf \
    -B:variant,VCF ./testdata/snps.raw31.vcf \
    -B:mask,Bed ./testdata/indels.mask31.bed \
    --maskName InDel \
    --clusterWindowSize 10 \
    --filterExpression "QUAL < 30.0 || AB > 0.75 && DP > 40 || QD < 5.0 || HRun > 5 || SB > -0.10" \
    --filterName "StandardFilters" \
    --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
    --filterName "HARD_TO_VALIDATE"

    I got this Error:
    ariantContextUtils.initializeMatchExps@223![15,17]: 'QUAL < 30.0 || AB > 0.75 && DP > 40 || QD < 5.0 || HRun > 5 || SB > -0.10;'
    undefined variable AB
    And I don't find the AB term in the snps.raw32.vcf file.
    How can I make GATK UnifiedGenotyper generate the snps.raw32.vcf contain the AB term?

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