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mutect2full.sh
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mutect2full.sh
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#!/bin/bash
while read -r line
do
name=${line%????};
## GLOBAL VARIABLES
INPUTBAM='outputBam'
MIDDIR='sortedBam'
OUTPUTDIR='mkDupGatk'
GENOME='./refGenome/GRCh38_filt.fa'
REFDICT='./refGenome/GRCh38_filt.dict'
INPUTMD='mkDupGatk'
GNOMAD='/mnt/md0/somatic-hg38-af-only-gnomad.hg38.vcf.gz'
BEDINTERVALS='/mnt/md0/humanGenome/TCGA/intervals.bed'
REFGENOME='/mnt/md0/humanGenome/TCGA/GRCh38.d1.vd1.fa'
VCFFILES='tmpVcfFiles'
PONFILE='/home/dtiezzi/ncbi/dbGaP-19480/mutect/gatk4_mutect2_4136_pon.vcf.gz'
OUTVCFS='vcfDir'
VCFSORTED='vcfSorted'
INPUTDIR='vcfFinal'
OUTDIR='mutcallFiltered'
FUNCOTATODATA='/home/dtiezzi/Softwares/gatk-4.1.6.0/funcotator_dataSources.v1.6.20190124s/'
# echo '[INFO] sorting ' $SAMPLE ' file...'
# samtools sort -n -@ 8 -o $MIDDIR/${name}.bam $INPUTBAM/${name}.bam ;
# samtools fixmate -m -@ 8 $MIDDIR/${name}.bam $MIDDIR/${name}_fixmate.bam
# samtools sort -@ 8 -o $MIDDIR/${name}_sorted.bam $MIDDIR/${name}_fixmate.bam
# echo '[INFO] removing duplicates from ' $SAMPLE ' file...'
# #samtools rmdup $MIDDIR/${name}_sorted.bam $INPUTBAM/${name}_RD.bam ;
# samtools markdup -r -@ 8 $MIDDIR/${name}_sorted.bam $INPUTBAM/${name}_RD.bam ;
# rm $MIDDIR/* ;
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# MarkDuplicatesSpark --input $INPUTBAM/${name}_RD.bam --output $OUTPUTDIR/${name}_001.bam --tmp-dir ./ ;
# echo '[INFO] Marking duplicates in ' $SAMPLE ' file...'
# java -jar /home/dtiezzi/Softwares/picard/build/libs/picard.jar MarkDuplicates \
# CREATE_INDEX=true \
# INPUT=$INPUTBAM/${name}_RD.bam \
# OUTPUT=$OUTPUTDIR/${name}_001.bam \
# METRICS_FILE=$OUTPUTDIR/${name}_marked_dup_metrics.txt \
# VALIDATION_STRINGENCY=STRICT
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# BaseRecalibrator -I $OUTPUTDIR/${name}_001.bam -R $REFGENOME \
# --known-sites snps/common_all_20180418.vcf.gz -O ${name}_recal_data.table ;
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# ApplyBQSR -R $REFGENOME -I $OUTPUTDIR/${name}_001.bam --bqsr-recal-file ${name}_recal_data.table -O $OUTPUTDIR/${name}_md.bam ;
# rm $OUTPUTDIR/${name}_RD.bam $OUTPUTDIR/${name}_001.bam
# echo '[INFO] starting analysis on' $name
# ## 1. Generate OXOG metrics:
# echo '[INFO] Step 1: ' $name
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# CollectSequencingArtifactMetrics \
# -I ./$INPUTMD/${name}_md.bam \
# -O ./OXO/$name \
# --FILE_EXTENSION .txt \
# -R $GENOME ;
# cp ./OXO/$name.pre_adapter_detail_metrics.txt ./vcfSorted ;
# ## 2. Generate pileup summaries on tumor sample:
# echo '[INFO] Step 2: ' $name
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# GetPileupSummaries \
# -I ./$INPUTMD/${name}_md.bam \
# -O ${name}.targeted_sequencing.table \
# -V $GNOMAD --intervals $BEDINTERVALS -R $GENOME ;
# ## 3. Calculate contamination on tumor sample
# echo '[INFO] Step 3: ' $name
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# CalculateContamination \
# -I ${name}.targeted_sequencing.table -O ./$VCFSORTED/${name}.targeted_sequencing.contamination.table ;
# ## 4. Find tumor sample name from BAM
# echo '[INFO] Step 4: ' $name
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# GetSampleName \
# -I $INPUTMD/${name}_md.bam \
# -O tumour.targeted_sequencing.${name} ;
# ## 5. Run MuTect2 using only tumor sample on chromosome level (25 commands with different intervals)
# echo '[INFO] Step 5 (MUTECT2 loop): ' $name
# while read -r line1;
# do
# chrL=$line1
# chr=$( echo "$chrL" |cut -d\: -f1 )
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-Djava.io.tmpdir=/tmp -XX:+UseSerialGC -Xmx3G" Mutect2 \
# -R $REFGENOME \
# -L $chrL -I ./$INPUTMD/${name}_md.bam \
# -O $VCFFILES/$chr.mt2.vcf \
# -tumor ${name} --af-of-alleles-not-in-resource 2.5e-06 \
# --germline-resource $GNOMAD \
# --f1r2-tar-gz f1r2/${name}_f1r2.tar.gz \
# -pon $PONFILE
# done < 'chrLengths' ;
# ## After this step, all chromosome level VCFs are merged into one.
# java -jar /home/dtiezzi/Softwares/picard/build/libs/picard.jar MergeVcfs \
# I=input_variant_files.list O=$OUTVCFS/$name.vcf.gz ;
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" MergeMutectStats --stats input_stats_files.list -O $VCFSORTED/$name.targeted_sequencing.mutect2.tumor_only.sorted.vcf.gz.stats ;
# mv $VCFSORTED/$name.targeted_sequencing.mutect2.tumor_only.sorted.vcf.gz.stats $VCFFINALDIR ;
# mv $VCFFINALDIR/$name.targeted_sequencing.mutect2.tumor_only.sorted.vcf.gz.stats $VCFFINALDIR/${name}.targeted_sequencing.tumor_only.gatk4_mutect2.raw_somatic_mutation.vcf.gz.stats ;
# ## 6. Sort VCF with Picard
# echo '[INFO] Step 6: ' $name
# java -jar /home/dtiezzi/Softwares/picard/build/libs/picard.jar SortVcf \
# SEQUENCE_DICTIONARY=$REFDICT \
# OUTPUT=$VCFSORTED/$name.targeted_sequencing.mutect2.tumor_only.sorted.vcf.gz I=$OUTVCFS/$name.vcf.gz
# cd $VCFSORTED ;
# ## 7. Filter variant calls from MuTect
# echo '[INFO] Step 7: ' $name
# /home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" \
# FilterMutectCalls \
# -R $REFGENOME \
# -O $name.targeted_sequencing.mutect2.tumor_only.contFiltered.vcf.gz \
# -V $name.targeted_sequencing.mutect2.tumor_only.sorted.vcf.gz --contamination-table $name.targeted_sequencing.contamination.table \
# -L $BEDINTERVALS ;
# ## 8. Filter variants by orientation bias
# echo '[INFO] Step 8: ' $name
# VCFFINALDIR='vcfFinal'
# /home/dtiezzi/Softwares/gatk-4.0.2.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" FilterByOrientationBias \
# -O ../$VCFFINALDIR/$name.targeted_sequencing.tumor_only.gatk4_mutect2.raw_somatic_mutation.vcf.gz \
# -P $name.pre_adapter_detail_metrics.txt -V $name.targeted_sequencing.mutect2.tumor_only.contFiltered.vcf.gz -L $BEDINTERVALS \
# -R $REFGENOME \
# -AM G/T \
# -AM C/T ;
# cd ..
echo '[INFO] Step 9: filtering ' $name 'sample...'
/home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" LearnReadOrientationModel -I f1r2/${name}_f1r2.tar.gz -O ${name}_read-orientation-model.tar.gz
/home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" FilterMutectCalls -V $INPUTDIR/${name}.targeted_sequencing.tumor_only.gatk4_mutect2.raw_somatic_mutation.vcf.gz -R $REFGENOME --ob-priors ${name}_read-orientation-model.tar.gz --min-allele-fraction 0.05 --unique-alt-read-count 10 -O $OUTDIR/${name}_somatic_filtered.vcf
grep -E "#|PASS" $OUTDIR/${name}_somatic_filtered.vcf > $OUTDIR/${name}_somatic_filtered_PASS.vcf
/home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" Funcotator -R $REFGENOME -V $OUTDIR/${name}_somatic_filtered_PASS.vcf -O $OUTDIR/${name}_somatic_annotated.vcf --output-file-format VCF --data-sources-path $FUNCOTATODATA --ref-version hg38
/home/dtiezzi/Softwares/gatk-4.1.6.0/gatk --java-options "-XX:+UseSerialGC -Xmx3G" Funcotator -R $REFGENOME -V $OUTDIR/${name}_somatic_filtered_PASS.vcf -O $OUTDIR/${name}_somatic_annotated.maf --output-file-format MAF --data-sources-path $FUNCOTATODATA --ref-version hg38 --annotation-override Tumor_Sample:${name}
echo '[INFO] Analysis DONE in ' $name
done < 'bamFiles'