142    ◾    Bioinformatics

--filter-name “QD2” \

-filter “QUAL<30.0” \

--filter-name “QUAL30” \

-filter “SOR>3.0” \

--filter-name “SOR3” \

-filter “FS>60.0” \

--filter-name “FS60” \

-filter “MQ<40.0” \

--filter-name “MQ40” \

-filter “MQRankSum<-12.5” \

--filter-name “MQRankSum-12.5” \

-filter “ReadPostRankSum<-8.0” \

--filter-name “ReadPostRankSum-8” \

-O filteredVCF/hardfilteredVCF.vcf

#The hard filtering GATK best prectice for INDEL

~/software/gatk-4.2.3.0/gatk \

--java-options \

-Xmx10G VariantFiltration \

-V vcf/allsamplesIndels_chr21.vcf \

-filter “QD<2.0” \

-- filter-name “QD2” \

-filter “QUAL<30.0” \

--filter-name “QUAL30” \

-filter “FS>200.0” \

--filter-name “FS200” \

-filter “ReadPostRankSum<-20.0” \

FIGURE 4.7  Visualizing InDels and SNPs with IGV.