mutations_caller_pipeline_aws 0.0.8 → 0.0.9
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@@ -8,7 +8,7 @@ class BwaCaller
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end
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def self.call_paired_end(r1, r2, out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
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-
cmd = "qsub -cwd -b y -N #{job_prefix}
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+
cmd = "qsub -cwd -b y -N bwa_#{job_prefix} -l h_vmem=9G -pe make 4 #{account}\
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#{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
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<(#{bwa} aln #{index} #{r1} 2>>#{log_file}) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
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#{r1} #{r2} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"
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@@ -3,7 +3,7 @@ class GatkCaller
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# Genotyper
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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}
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+
qsub -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=3G -hold_jid recalibration_#{job_prefix} #{account}\
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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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@@ -16,7 +16,7 @@ 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}
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+
qsub -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=4G -hold_jid realignment_#{job_prefix} #{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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@@ -29,7 +29,7 @@ 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}
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+
qsub -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=4G -hold_jid recalibration_table_#{job_prefix} #{account} \
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#{gatk} \
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-R #{index_fa} \
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-I #{read_bam} \
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@@ -43,7 +43,7 @@ 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}
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qsub -cwd -b y -N prep_realignment_#{job_prefix} -l h_vmem=4G -hold_jid indexing_#{job_prefix} #{account}\
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#{gatk} \
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-I #{read_bam} \
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-R #{index_fa} \
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@@ -56,7 +56,7 @@ 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}
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qsub -cwd -b y -N realignment_#{job_prefix} -l h_vmem=4G -hold_jid prep_realignment_#{job_prefix} #{account} \
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#{gatk} \
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-I #{read_bam} \
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-R #{index_fa} \
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@@ -1,6 +1,6 @@
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class SamtoolsIndexing
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def self.call(bam_file, job_prefix, account, debug)
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cmd = "qsub -cwd -b y -N #{job_prefix}
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cmd = "qsub -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
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samtools index #{bam_file}"
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puts cmd
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system(cmd) if debug == 1
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