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1.reseq

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1.reseq [2017/12/15 15:33] – created hyjeong1.reseq [2021/03/17 13:09] (current) – external edit 127.0.0.1
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   #########################   #########################
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   #   2017 C&K Workshop   #   #   2017 C&K Workshop   #
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   #   Resequencing Code   #   #   Resequencing Code   #
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   #        2017. 11       #   #        2017. 11       #
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   #########################   #########################
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   ########Resequencing ###########   ########Resequencing ###########
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   cd /home/workshop/1.WGS_practice/Genome_analysis   cd /home/workshop/1.WGS_practice/Genome_analysis
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   ### FASTQC   ### FASTQC
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   fastqc --nogroup paired_end_sep1.fq paired_end_sep2.fq   fastqc --nogroup paired_end_sep1.fq paired_end_sep2.fq
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   ### TRIMMOMATIC   ### TRIMMOMATIC
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   java -jar /home/Program/Trimmomatic-0.33/trimmomatic-0.33.jar \   java -jar /home/Program/Trimmomatic-0.33/trimmomatic-0.33.jar \
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   PE paired_end_sep1.fq paired_end_sep2.fq paired_end_1P.fastq.gz paired_end_1U.fastq.gz \   PE paired_end_sep1.fq paired_end_sep2.fq paired_end_1P.fastq.gz paired_end_1U.fastq.gz \
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   paired_end_2P.fastq.gz paired_end_2U.fastq.gz \   paired_end_2P.fastq.gz paired_end_2U.fastq.gz \
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   ILLUMINACLIP:/home/Program/Trimmomatic-0.33/adapters/total-TruSeq-PE.fa:2:30:10 \   ILLUMINACLIP:/home/Program/Trimmomatic-0.33/adapters/total-TruSeq-PE.fa:2:30:10 \
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   TRAILING:20 MINLEN:75   TRAILING:20 MINLEN:75
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   ### REFERENCE INDEXING   ### REFERENCE INDEXING
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   /home/Program/bowtie2-2.2.5/bowtie2-build Reference.fa Reference   /home/Program/bowtie2-2.2.5/bowtie2-build Reference.fa Reference
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   ### READ MAPPING   ### READ MAPPING
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   /home/Program/bowtie2-2.2.5/bowtie2 \   /home/Program/bowtie2-2.2.5/bowtie2 \
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   -x Reference \   -x Reference \
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   -1 paired_end_1P.fastq.gz -2 paired_end_2P.fastq.gz \   -1 paired_end_1P.fastq.gz -2 paired_end_2P.fastq.gz \
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   -S paired_end.sam \   -S paired_end.sam \
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   2> /home/workshop/1.WGS_practice/Genome_analysis/paired_end.bowtie2stat   2> /home/workshop/1.WGS_practice/Genome_analysis/paired_end.bowtie2stat
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   ### ADD_RG    ### ADD_RG 
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   java -jar /home/Program/picard-tools-1.138/picard.jar AddOrReplaceReadGroups \   java -jar /home/Program/picard-tools-1.138/picard.jar AddOrReplaceReadGroups \
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   INPUT=paired_end.sam \   INPUT=paired_end.sam \
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   OUTPUT=paired_end_RG.bam \   OUTPUT=paired_end_RG.bam \
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   SORT_ORDER=coordinate RGID=paired_end RGLB=paired_end RGPL=illumina RGPU=non RGSM=paired_end \   SORT_ORDER=coordinate RGID=paired_end RGLB=paired_end RGPL=illumina RGPU=non RGSM=paired_end \
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   VALIDATION_STRINGENCY=LENIENT   VALIDATION_STRINGENCY=LENIENT
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   ### REMOVE_DU   ### REMOVE_DU
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   java -jar /home/Program/picard-tools-1.138/picard.jar MarkDuplicates \   java -jar /home/Program/picard-tools-1.138/picard.jar MarkDuplicates \
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   INPUT=paired_end_RG.bam \   INPUT=paired_end_RG.bam \
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   OUTPUT=paired_end_RG_DU.bam \   OUTPUT=paired_end_RG_DU.bam \
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   METRICS_FILE=paired_end_RG_DU.metrics REMOVE_DUPLICATES=true ASSUME_SORTED=true \   METRICS_FILE=paired_end_RG_DU.metrics REMOVE_DUPLICATES=true ASSUME_SORTED=true \
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   VALIDATION_STRINGENCY=LENIENT    VALIDATION_STRINGENCY=LENIENT 
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   ### FIXMATE   ### FIXMATE
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   java -jar /home/Program/picard-tools-1.138/picard.jar FixMateInformation \   java -jar /home/Program/picard-tools-1.138/picard.jar FixMateInformation \
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   INPUT=paired_end_RG_DU.bam \   INPUT=paired_end_RG_DU.bam \
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   OUTPUT=paired_end_RG_DU_FIX.bam \   OUTPUT=paired_end_RG_DU_FIX.bam \
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   SORT_ORDER=coordinate \   SORT_ORDER=coordinate \
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   VALIDATION_STRINGENCY=LENIENT   VALIDATION_STRINGENCY=LENIENT
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   ### INDEXING   ### INDEXING
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   /home/Program/samtools-1.2/samtools faidx Reference.fa   /home/Program/samtools-1.2/samtools faidx Reference.fa
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   /home/Program/samtools-1.2/samtools index paired_end_RG_DU_FIX.bam   /home/Program/samtools-1.2/samtools index paired_end_RG_DU_FIX.bam
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   ### REALIGN   ### REALIGN
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T RealignerTargetCreator \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T RealignerTargetCreator \
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   -R Reference.fa \   -R Reference.fa \
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   -I paired_end_RG_DU_FIX.bam \   -I paired_end_RG_DU_FIX.bam \
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   -o paired_end_RG_DU_FIX_Realign.intervals    -o paired_end_RG_DU_FIX_Realign.intervals 
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T IndelRealigner \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T IndelRealigner \
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   -R Reference.fa \   -R Reference.fa \
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   -I paired_end_RG_DU_FIX.bam \   -I paired_end_RG_DU_FIX.bam \
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   -o paired_end_RG_DU_FIX_Realign.bam \   -o paired_end_RG_DU_FIX_Realign.bam \
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   -targetIntervals paired_end_RG_DU_FIX_Realign.intervals   -targetIntervals paired_end_RG_DU_FIX_Realign.intervals
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   ### BQ_RECAL   ### BQ_RECAL
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T BaseRecalibrator \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T BaseRecalibrator \
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   -R Reference.fa \   -R Reference.fa \
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   -I paired_end_RG_DU_FIX_Realign.bam \   -I paired_end_RG_DU_FIX_Realign.bam \
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   -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate \   -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate \
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   -knownSites Reference.vcf \   -knownSites Reference.vcf \
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   -o paired_end_RECAL.grp   -o paired_end_RECAL.grp
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T PrintReads \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T PrintReads \
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   -R Reference.fa \   -R Reference.fa \
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   -I paired_end_RG_DU_FIX_Realign.bam \   -I paired_end_RG_DU_FIX_Realign.bam \
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   -BQSR paired_end_RECAL.grp \   -BQSR paired_end_RECAL.grp \
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   -o paired_end_RECAL.bam   -o paired_end_RECAL.bam
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   ### INDEXING   ### INDEXING
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   /home/Program/samtools-1.2/samtools index paired_end_RECAL.bam   /home/Program/samtools-1.2/samtools index paired_end_RECAL.bam
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   ### IGV   ### IGV
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   java -Xmx1500m -jar /home/Program/IGV_2.3.80/igv.jar   java -Xmx1500m -jar /home/Program/IGV_2.3.80/igv.jar
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   ############ VARIANT CALLING #########   ############ VARIANT CALLING #########
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T UnifiedGenotyper \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T UnifiedGenotyper \
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   -R Reference.fa \   -R Reference.fa \
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   -I paired_end_RECAL.bam \   -I paired_end_RECAL.bam \
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   -o sample01.raw.vcf \   -o sample01.raw.vcf \
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   -glm BOTH   -glm BOTH
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \
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   -R Reference.fa \   -R Reference.fa \
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   -T SelectVariants \   -T SelectVariants \
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   --variant sample01.raw.vcf \   --variant sample01.raw.vcf \
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   -o snp_sample01.raw.vcf \   -o snp_sample01.raw.vcf \
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   -selectType SNP   -selectType SNP
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \
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   -R Reference.fa \   -R Reference.fa \
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   -T SelectVariants \   -T SelectVariants \
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   --variant sample01.raw.vcf \   --variant sample01.raw.vcf \
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   -o indel_sample01.raw.vcf \   -o indel_sample01.raw.vcf \
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   -selectType INDEL   -selectType INDEL
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   ### VARIANT FILTERING   ### VARIANT FILTERING
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \
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   -R Reference.fa \   -R Reference.fa \
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   -T VariantFiltration \   -T VariantFiltration \
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   --variant indel_sample01.raw.vcf \   --variant indel_sample01.raw.vcf \
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   -o filtered_indel_sample01.vcf \   -o filtered_indel_sample01.vcf \
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   --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0*DP)) > 0.1)" --filterName "HARD_TO_VALIDATE" \   --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0*DP)) > 0.1)" --filterName "HARD_TO_VALIDATE" \
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   --filterExpression "QUAL < 30" --filterName "QualFilter" \   --filterExpression "QUAL < 30" --filterName "QualFilter" \
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   --filterExpression "QD < 5.0" --filterName "QD5" \   --filterExpression "QD < 5.0" --filterName "QD5" \
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   --filterExpression "FS > 200.0" --filterName "FS200"    --filterExpression "FS > 200.0" --filterName "FS200" 
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   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \   java -jar /home/Program/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar \
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   -R Reference.fa \   -R Reference.fa \
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   -T VariantFiltration \   -T VariantFiltration \
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   --variant snp_sample01.raw.vcf \   --variant snp_sample01.raw.vcf \
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   -o filtered_snp_sample01.vcf \   -o filtered_snp_sample01.vcf \
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   --clusterSize 3 --clusterWindowSize 10 \   --clusterSize 3 --clusterWindowSize 10 \
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   --mask filtered_indel_sample01.vcf --maskName "InDel" \   --mask filtered_indel_sample01.vcf --maskName "InDel" \
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   --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0*DP)) > 0.1)" --filterName "HARD_TO_VALIDATE" \   --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0*DP)) > 0.1)" --filterName "HARD_TO_VALIDATE" \
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   --filterExpression "QUAL < 30" --filterName "QualFilter" \   --filterExpression "QUAL < 30" --filterName "QualFilter" \
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   --filterExpression "FS > 200.0 " --filterName "FS200"   --filterExpression "FS > 200.0 " --filterName "FS200"
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   ### VARIANT ANNOTATION   ### VARIANT ANNOTATION
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   #java -jar /home/Program/snpEff/snpEff.jar databases | more   #java -jar /home/Program/snpEff/snpEff.jar databases | more
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   #java -jar /home/Program/snpEff/snpEff.jar -download GRCh38.82   #java -jar /home/Program/snpEff/snpEff.jar -download GRCh38.82
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   java -jar /home/Program/snpEff/snpEff.jar Human3 filtered_snp_sample01.vcf -s filtered_snp_sample01.ann.html >filtered_snp_sample01.ann.vcf   java -jar /home/Program/snpEff/snpEff.jar Human3 filtered_snp_sample01.vcf -s filtered_snp_sample01.ann.html >filtered_snp_sample01.ann.vcf
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   java -jar /home/Program/snpEff/snpEff.jar Human3 filtered_indel_sample01.vcf -s filtered_indel_sample01.ann.html >filtered_indel_sample01.ann.vcf   java -jar /home/Program/snpEff/snpEff.jar Human3 filtered_indel_sample01.vcf -s filtered_indel_sample01.ann.html >filtered_indel_sample01.ann.vcf
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   ### IGV   ### IGV
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   java -Xmx1500m -jar /home/Program/IGV_2.3.80/igv.jar   java -Xmx1500m -jar /home/Program/IGV_2.3.80/igv.jar
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   ### END ###   ### END ###
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