Class: GatkCaller

Inherits:
Object
  • Object
show all
Defined in:
lib/mutations_caller_pipeline/gatk_caller.rb

Class Method Summary collapse

Class Method Details

.call(log_dir, gatk, index_fa, read_bam, read_vcf) ⇒ Object

INDEX is normal genom.fa



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# File 'lib/mutations_caller_pipeline/gatk_caller.rb', line 3

def self.call(log_dir, gatk, index_fa, read_bam, read_vcf)
  cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
    java -Xmx4g -jar  #{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
    -I #{read_bam} \
    -o #{read_vcf} \
    --genotype_likelihoods_model BOTH \
    >> #{log_dir} 2>&1 || exit 1"
  puts cmd
  system(cmd)
end

.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals) ⇒ Object 



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# File 'lib/mutations_caller_pipeline/gatk_caller.rb', line 36

def self.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals)
  cmd = "java -Xmx2g -jar #{gatk} \
    -I #{read_bam} \
    -R #{index_fa} \
    -T RealignerTargetCreator \
    -o #{target_intervals}"
  puts cmd
  system(cmd)
end

.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam) ⇒ Object 



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# File 'lib/mutations_caller_pipeline/gatk_caller.rb', line 46

def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam)
  cmd = "java -Xmx4g -jar #{gatk} \
    -I #{read_bam} \
    -R #{index_fa} \
    -T IndelRealigner \
    -targetIntervals #{target_intervals} \
    -o #{realigned_bam} >> #{log_dir} 2>&1 || exit 1"
  puts cmd
  system(cmd)
end

.recalibrate_bam(log_dir, gatk, index_fa, index_vcf, read_bam, recal_file) ⇒ Object 



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# File 'lib/mutations_caller_pipeline/gatk_caller.rb', line 14

def self.recalibrate_bam(log_dir ,gatk, index_fa, index_vcf, read_bam, recal_file )
  cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
    java -Xmx4g -jar #{gatk} -knownSites #{index_vcf} -I #{read_bam} \
    -R #{index_fa} -T CountCovariates \
    -cov ReadGroupCovariate -cov QualityScoreCovariate -cov DinucCovariate \
    -cov CycleCovariate \
    -recalFile #{recal_file} >> #{log_dir} 2>&1 || exit 1 "
  puts cmd
  system(cmd)
end

.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file) ⇒ Object 



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# File 'lib/mutations_caller_pipeline/gatk_caller.rb', line 25

def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file)
  cmd = "java -Xmx4g -jar #{gatk} \
    -R #{index_fa} \
    -I #{read_bam} \
    -T TableRecalibration \
    -o #{recal_bam} \
    -recalFile #{recal_file} >> #{log_dir} 2>&1 || exit 1"
  puts cmd
  system(cmd)
end