class GatkCaller
Public Class Methods
call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account,dbsnp_file, debug)
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INDEX is normal genom.fa Genotyper
# File lib/mutations_caller_pipeline_aws/gatk_caller.rb, line 4 def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account,dbsnp_file, debug) cmd = "qsub -pe DJ 4 -o #{log_dir} -e #{log_dir}_genotyper_errors -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=6G -hold_jid recalibration_#{job_prefix} #{account}\ java -Xmx6g -jar #{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \ -I #{read_bam} --dbsnp #{dbsnp_file} \ -o #{read_vcf} -nt 4 --max_alternate_alleles 8 \ --genotype_likelihoods_model BOTH" puts cmd system(cmd) if debug == 1 end
coverage(log_dir, gatk, index_fa, read_bam, outfile_prefix, job_prefix, account, debug)
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INDEX is normal genom.fa Coverage Summary parallel not possible yet (1.6-13-g91f02df)
# File lib/mutations_caller_pipeline_aws/gatk_caller.rb, line 17 def self.coverage(log_dir, gatk, index_fa, read_bam, outfile_prefix, job_prefix, account, debug) cmd = "qsub -o #{log_dir} -e #{log_dir}_coverage_errors -V -cwd -b y -N coverage_#{job_prefix} -l h_vmem=14G -hold_jid recalibration_#{job_prefix} #{account}\ java -Xmx6g -jar #{gatk} -R #{index_fa} -T DepthOfCoverage \ -I #{read_bam} --omitDepthOutputAtEachBase \ -o #{outfile_prefix} --omitIntervalStatistics --omitLocusTable" puts cmd system(cmd) if debug == 1 end
prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals, job_prefix, account, dbsnp_file, debug)
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Preparation realignement
# File lib/mutations_caller_pipeline_aws/gatk_caller.rb, line 52 def self.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals, job_prefix, account, dbsnp_file, debug) cmd = "qsub -pe DJ 4 -o #{log_dir} -e #{log_dir}_prep_realign_errors -V -cwd -b y -N prep_realignment_#{job_prefix} -l h_vmem=6G -hold_jid index_#{job_prefix} #{account}\ java -Xmx6g -jar #{gatk} -nt 4 \ -I #{read_bam} --known #{dbsnp_file} \ -R #{index_fa} \ -T RealignerTargetCreator \ -o #{target_intervals}" puts cmd system(cmd) if debug == 1 end
realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug)
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Realignment parallel not possible yet (1.6-13-g91f02df)
# File lib/mutations_caller_pipeline_aws/gatk_caller.rb, line 65 def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug) cmd = "qsub -o #{log_dir} -e #{log_dir}_realign_errors -V -cwd -b y -N realignment_#{job_prefix} -l h_vmem=14G -hold_jid prep_realignment_#{job_prefix} #{account} \ java -Xmx6g -jar #{gatk} \ -I #{read_bam} \ -R #{index_fa} \ -T IndelRealigner \ -targetIntervals #{target_intervals} \ -o #{realigned_bam}" puts cmd system(cmd) if debug == 1 end
recalibrate_bam(log_dir ,gatk, index_fa, read_bam, recal_file, job_prefix, account, dbsnp_file, debug )
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Making recalibration table
# File lib/mutations_caller_pipeline_aws/gatk_caller.rb, line 27 def self.recalibrate_bam(log_dir ,gatk, index_fa, read_bam, recal_file, job_prefix, account, dbsnp_file, debug ) cmd = "qsub -o #{log_dir} -e #{log_dir}_recalibrate_errors -V -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=14G -hold_jid realignment_#{job_prefix} #{account} \ java -Xmx6g -jar #{gatk} -knownSites #{dbsnp_file} -I #{read_bam} \ -R #{index_fa} -T BaseRecalibrator \ -o #{recal_file}" puts cmd system(cmd) if debug == 1 end
table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug)
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Using recalibration table parallel not possible yet (1.6-13-g91f02df)
# File lib/mutations_caller_pipeline_aws/gatk_caller.rb, line 38 def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug) cmd = "qsub -V -o #{log_dir} -e #{log_dir}_prep_recal_errors -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=14G -hold_jid recalibration_table_#{job_prefix} #{account} \ java -Xmx6g -jar #{gatk} \ -R #{index_fa} \ -I #{read_bam} \ -T PrintReads \ -o #{recal_bam} \ -BQSR #{recal_file}" puts cmd system(cmd) if debug == 1 end