Generate genotype

= Generate genotype = Using GATK to call all.vcf file

java -Xmx${heap}m \ -jar $gatk \ -R $REF \ -T UnifiedGenotyper \ --dbsnp $DBSNP \ -I $PWDS/${subjectID}.realigned.recal.bam \ --out $PWDS/${subjectID}.snps.raw.all.vcf \ -stand_call_conf 30.0 \ -stand_emit_conf 10.0 \ -l INFO \ -A DepthOfCoverage \ -A HaplotypeScore \ -A InbreedingCoeff \ -glm SNP \ -nt 1 \ -L $ExonFile \ -U ALLOW_UNINDEXED_BAM \ --output_mode EMIT_ALL_CONFIDENT_SITES Using GATK to filter to vcf.all file and generate all.PASS.vcf file

java -Xmx${heap}m \ -jar $gatk \ -T VariantFiltration \ -R $REF \ -o $PWDS/${subjectID}.snps.all.vcf \ --variant $PWDS/${subjectID}.snps.raw.all.vcf \ --mask $PWDS/variants/${subjectID}.indels.PASS.vcf \ --maskName InDel \ --filterExpression "QD < 2.0" \ --filterName "QDFilter" \ --filterExpression "MQ < 40.0" \ --filterName "MQFilter" \ --filterExpression "FS > 60.0" \ --filterName "FSFilter" \ --filterExpression "HaplotypeScore > 13.0" \ --filterName "HaplotypeScoreFilter" \ --filterExpression "MQRankSum < -12.5" \ --filterName "MQRankSumFilter" \ --filterExpression "ReadPosRankSum < -8.0" \ --filterName "ReadPosRankSumFilter" \ --filterExpression "QUAL < 30.0 || DP < 6 || DP > 5000 || HRun > 5" \ --filterName "StandardFilters" \ --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \ --filterName "HARD_TO_VALIDATE" \ -l OFF mline=`grep -n "#CHROM" $PWDS/${subjectID}.snps.all.vcf | cut -d':' -f 1` head -n $mline $PWDS/${subjectID}.snps.all.vcf > $PWDS/head.vcf cat $PWDS/${subjectID}.snps.all.vcf |  \ grep PASS | cat $PWDS/head.vcf - >  \ $PWDS/${subjectID}.snps.all.PASS.vcf Remove intermediate and index files rm -f $PWDS/head.vcf rm -f $PWDS/${subjectID}.snps.vcf rm -f $PWDS/${subjectID}.snps.raw.all.vcf rm -f $PWDS/*.idx rm -f $subjectDir/*.idx rm -f $PWDS/variants/*.idx

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