Calling variants UGVR

UnifiedGenotyper Group Calling and Variant Recalibration

UnifiedGenotyper Group Calling
java -Xmx32g -Djava.io.tmpdir=/md1/BSI-SZ/analysis/tmp1 \ -jar $GATK \ -l INFO -L $targets_intervals -nt 2  \ -R $hg19_ref \ -I /md1/D12PEACXX_1_ACAGTG.realigned.recal.bam.g.bam \ -I /md1/D12PEACXX_1_ACTTGA.realigned.recal.bam.g.bam \ . . (list all bam files here) . -I /md1/D12PEACXX_8_TAGCTT.realigned.recal.bam.g.bam \ -I /md1/D12PEACXX_8_TGACCA.realigned.recal.bam.g.bam \ -I /md1/D12PEACXX_8_TTAGGC.realigned.recal.bam.g.bam \ --dbsnp $dbsnp \ -T UnifiedGenotyper -glm $glmmode \ -dcov 250 -out_mode EMIT_VARIANTS_ONLY \ --max_alternate_alleles 10 \ -o $outfile \ -stand_call_conf 30 -stand_emit_conf 10
 * 1) SNPs

java -Xmx32g -Djava.io.tmpdir=/md1/BSI-SZ/analysis/tmp2 \ -jar $GATK \ -l INFO -L $targets_intervals -nt 8  \ -R $hg19_ref \ -I /md1/D12PEACXX_1_ACAGTG.realigned.recal.bam.g.bam \ -I /md1/D12PEACXX_1_ACTTGA.realigned.recal.bam.g.bam \ -I /md1/D12PEACXX_1_ATCACG.realigned.recal.bam.g.bam \ . . (list all bam files here) . -I /md1/D12PEACXX_8_TGACCA.realigned.recal.bam.g.bam \ -I /md1/D12PEACXX_8_TTAGGC.realigned.recal.bam.g.bam \ --dbsnp $dbsnp \ -T UnifiedGenotyper -glm $glmmode \ -dcov 250 -out_mode EMIT_VARIANTS_ONLY \ --max_alternate_alleles 10 \ -o $outfile \ -stand_call_conf 30 -stand_emit_conf 10
 * 1) Indels

Variant Recalibration
java -Xmx32g -Djava.io.tmpdir=$wdir/tmp1               \ -jar $GATK/GenomeAnalysisTK.jar                      \ -l INFO -L $targets_intervals -nt 4                  \ -R $hg19_ref                                         \ -T VariantRecalibrator                               \ -input $wdir/$input_rawSNP                           \ --maxGaussians 6                                     \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0  \ $GATK/resources/hg19/hapmap_3.3.hg19.vcf         \ -resource:omni,known=false,training=true,truth=false,prior=12.0    \ $GATK/resources/hg19/1000G_omni2.5.hg19.vcf      \ -resource:dbsnp,known=true,training=false,truth=false,prior=6.0    \ $GATK/resources/hg19/dbsnp_137.hg19.vcf          \ -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an DP       \ -an InbreedingCoeff -an HaplotypeScore                             \ -mode SNP                                                          \ -recalFile    $wdir/bsi.SNPrecal.vcf                               \ -tranchesFile $wdir/bsi.SNPrecal.tranches                          \ -rscriptFile  $wdir/bsi.SNPrecal.plots.R
 * 1) Variant Recalibrator for SNPs

java -Xmx32g -Djava.io.tmpdir=$wdir/tmp2               \ -jar $GATK/GenomeAnalysisTK.jar                      \ -l INFO -L $targets_intervals -nt 4                  \ -R $hg19_ref                                         \ -T VariantRecalibrator                               \ -input $wdir/$input_rawINDEL                         \ --maxGaussians 1                                     \ -percentBad 0.15 --minNumBadVariants 500             \ -resource:mills,VCF,known=false,training=true,truth=true,prior=12.0    \ $GATK/resources/hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf    \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0    \ $GATK/resources/hg19/dbsnp_137.hg19.vcf      \ -an DP -an FS -an ReadPosRankSum -an MQRankSum                \ -an QD -an ReadPosRankSum                                     \ -an InbreedingCoeff                                           \ -mode INDEL                                                   \ -recalFile    $wdir/bsi.Indelrecal.vcf                        \ -tranchesFile $wdir/bsi.Indelrecal.tranches                   \ -rscriptFile  $wdir/bsi.Indelrecal.plots.R
 * 1) Variant Recalibrator for Indels

Apply Recalibration
java -Xmx32g -Djava.io.tmpdir=$wdir/tmp1   \ -jar $GATK/GenomeAnalysisTK.jar          \ -l INFO -L $targets_intervals -nt 4      \ -R $hg19_ref                             \ -T ApplyRecalibration                    \ -input $wdir/$input_rawSNP               \ --ts_filter_level 99.0                   \ -recalFile   $wdir/bsi.SNPrecal.vcf      \ -tranchesFile $wdir/bsi.SNPrecal.tranches \ -mode SNP                                \ -o $wdir/bsi.VarRecalfiltSNP.vcf
 * 1) Apply Recalibration for SNPs

java -Xmx32g -Djava.io.tmpdir=$wdir/tmp2         \ -jar $GATK/GenomeAnalysisTK.jar                \ -l INFO -L $targets_intervals -nt 4            \ -R $hg19_ref                                   \ -T ApplyRecalibration                          \ -input $wdir/$input_rawINDEL                   \ --ts_filter_level 95.0                         \ -recalFile   $wdir/bsi.Indelrecal.vcf          \ -tranchesFile $wdir/bsi.Indelrecal.tranches    \ -mode INDEL                                    \ -o $wdir/bsi.VarRecalfiltIndel.vcf
 * 1) Apply Recalibration for Indels

Variant Eval
java -Xmx32g -Djava.io.tmpdir=$wdir/tmp1 \ -jar $GATK/GenomeAnalysisTK.jar       \ -l INFO -L $targets_intervals -nt 4   \ -R $hg19_ref                          \ -T VariantEval                        \ --dbsnp $dbsnp_ex                     \ -eval $wdir/bsi.VarRecalfiltSNP.vcf   \ -o    $wdir/bsi.Final_SNP.gatkreport
 * 1) Variant Eval for SNPs

java -Xmx32g -Djava.io.tmpdir=$wdir/tmp2  \ -jar $GATK/GenomeAnalysisTK.jar         \ -l INFO -L $targets_intervals -nt 4     \ -R $hg19_ref                            \ -T VariantEval                          \ --dbsnp $dbsnp_ex                       \ -eval  $wdir/bsi.VarRecalfiltIndel.vcf  \ -o     $wdir/bsi.Final_Indel.gatkreport
 * 1) Variant Eval for Indels

< Back to Whole Exome Sequencing Analysis Pipeline