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?
-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?