mutations_caller_pipeline_aws 0.0.7 → 0.0.8
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@@ -4,7 +4,7 @@ class GatkCaller
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def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account, debug)
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cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
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qsub -cwd -b y -N #{job_prefix}_genotyper -l h_vmem=3G -hold_jid #{job_prefix}_recalibration #{account}\
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-
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+
#{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
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-I #{read_bam} \
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-o #{read_vcf} \
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--genotype_likelihoods_model BOTH \
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@@ -16,8 +16,8 @@ class GatkCaller
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# Making recalibration table
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def self.recalibrate_bam(log_dir ,gatk, index_fa, index_vcf, read_bam, recal_file, job_prefix, account, debug )
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cmd = "echo 'starting recalibration table ' `date` >> #{log_dir}
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-
qsub -cwd -b y -N #{job_prefix}_recalibration_table -l h_vmem=
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-
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qsub -cwd -b y -N #{job_prefix}_recalibration_table -l h_vmem=4G #{account} \
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#{gatk} -knownSites #{index_vcf} -I #{read_bam} \
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-R #{index_fa} -T CountCovariates \
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-cov ReadGroupCovariate -cov QualityScoreCovariate -cov DinucCovariate \
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-cov CycleCovariate \
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@@ -29,8 +29,8 @@ class GatkCaller
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# Using recalibration table
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def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug)
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cmd = "echo 'recalibrating bam_file at ' `date` >> #{log_dir}
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qsub -cwd -b y -N #{job_prefix}_recalibration -l h_vmem=
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-
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qsub -cwd -b y -N #{job_prefix}_recalibration -l h_vmem=4G -hold_jid #{job_prefix}_recalibration_table #{account} \
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#{gatk} \
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-R #{index_fa} \
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-I #{read_bam} \
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-T TableRecalibration \
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@@ -43,8 +43,8 @@ class GatkCaller
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# Preparation realignement
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def self.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals, job_prefix, account, debug)
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cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
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-
qsub -cwd -b y -N #{job_prefix}_prep_realignment -l h_vmem=
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-
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qsub -cwd -b y -N #{job_prefix}_prep_realignment -l h_vmem=4G -hold_jid #{job_prefix}_indexing #{account}\
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#{gatk} \
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-I #{read_bam} \
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-R #{index_fa} \
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-T RealignerTargetCreator \
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@@ -56,8 +56,8 @@ class GatkCaller
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# Realignment
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def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug)
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cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
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-
qsub -cwd -b y -N #{job_prefix}_realignment -l h_vmem=
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-
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qsub -cwd -b y -N #{job_prefix}_realignment -l h_vmem=4G -hold_jid #{job_prefix}_prep_realignment #{account} \
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#{gatk} \
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-I #{read_bam} \
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-R #{index_fa} \
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-T IndelRealigner \
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