Indel filter

java -Xmx32g -jar $HOME/tool/gatk/GenomeAnalysisTK.jar -T VariantFiltration -R $HOME/data/hg19.fasta \

-o x1.indel.filtered.vcf \

-B:variant,VCF x1.indel.vcf \

-B:mask,VCF ../SNP/x1.snp.vcf \

--maskName SNP \

--filterExpression "QUAL < 30 || SB > -1.0 || QD < 2.0" \

--filterName "QUAL<30;SB>-1.0;QD<2"