Demo entry 6624486



Submitted by anonymous on Jun 16, 2017 at 09:33
Language: Bash. Code size: 2.0 kB.

echo ====2.1.Germline Variant_HC====
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -I $BatchFolder/bam/$ -R $genome --genotyping_mode DISCOVERY --dbsnp $dbsnp_hg19 -stand_call_conf 30 -stand_emit_conf 10 -o $BatchFolder/vcf/$sampleName.HCvariants.vcf -L $TargetRegion
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T SelectVariants -R $genome --variant $BatchFolder/vcf/$sampleName.HCvariants.vcf -o $BatchFolder/vcf/$sampleName.HCvariants.indel.vcf -selectType INDEL
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T SelectVariants -R $genome --variant $BatchFolder/vcf/$sampleName.HCvariants.vcf -o $BatchFolder/vcf/$sampleName.HCvariants.snp.vcf -selectType SNP
        echo "done HC variant calling"

        echo ===2.2.hard filter_HC==
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $genome -V $BatchFolder/vcf/$sampleName.HCvariants.snp.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "my_snp_filter" -o $BatchFolder/vcf/$sampleName.HCvariants.snp.filtered.vcf
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T SelectVariants -R $genome --variant $BatchFolder/vcf/$sampleName.HCvariants.snp.filtered.vcf -o $BatchFolder/vcf/$sampleName.HCvariants.snp.filtered.Panel.vcf -L $TargetRegion
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $genome -V $BatchFolder/vcf/$sampleName.HCvariants.indel.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "my_indel_filter" -o $BatchFolder/vcf/$sampleName.HCvariants.indel.filtered.vcf
        java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar -T SelectVariants -R $genome --variant $BatchFolder/vcf/$sampleName.HCvariants.indel.filtered.vcf -o $BatchFolder/vcf/$sampleName.HCvariants.indel.filtered.Panel.vcf -L $TargetRegion
        echo "done HC variant calling

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