class GatkCaller

Public Class Methods

call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account,dbsnp_file, debug) click to toggle source

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) click to toggle source

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) click to toggle source

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) click to toggle source

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 ) click to toggle source

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) click to toggle source

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