mutations_caller_pipeline_aws 0.0.14 → 0.0.15

data/bin/mutations_caller_pipeline_aws

@@ -225,6 +225,7 @@ GatkCaller.table_calibration(log_file,
 GatkCaller.call(log_file,
                 options[:gatk],
                 options[:index_fa],
+                options[:index_vcf],
                 recal_bam,
                 options[:vcf],
                 job_prefix,

data/lib/mutations_caller_pipeline_aws/gatk_caller.rb

@@ -1,11 +1,12 @@
 class GatkCaller
   # INDEX is normal genom.fa
   # Genotyper
-  def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account, debug)
+  def self.call(log_dir, gatk, index_fa, dbSNP, read_bam, read_vcf, job_prefix, account, debug)
     cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
       qsub -o #{log_dir} -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=4.5G -hold_jid recalibration_#{job_prefix} #{account}\
       #{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
       -I #{read_bam} \
+      -D #{dbSNP}
       -o #{read_vcf} \
       --genotype_likelihoods_model BOTH"
     puts cmd
@@ -16,7 +17,7 @@ class GatkCaller
   # Coverage Summary
   def self.coverage(log_dir, gatk, index_fa, read_bam, outfile_prefix, job_prefix, account, debug)
     cmd = "echo 'starting coverage GATK for mutant at ' `date` >> #{log_dir}
-      qsub -o #{log_dir} -V -cwd -b y -N genotyper_#{job_prefix} -l h_vmem=4.5G -hold_jid recalibration_#{job_prefix} #{account}\
+      qsub -o #{log_dir} -V -cwd -b y -N coverage_#{job_prefix} -l h_vmem=4.5G -hold_jid recalibration_#{job_prefix} #{account}\
       #{gatk} -R #{index_fa} -T DepthOfCoverage \
       -I #{read_bam} \
       -o #{outfile_prefix} "

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version 
-  hash: 3
+  hash: 1
   prerelease: 
   segments: 
   - 0
   - 0
-  - 14
-  version: 0.0.14
+  - 15
+  version: 0.0.15
 platform: ruby
 authors: 
 - Kaharina Hayer