class PicardCaller
Public Class Methods
build_index
= “java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/BuildBamIndex.jar I=marked_dublicates.bam VALIDATION_STRINGENCY=LENIENT”
# File lib/mutations_caller_pipeline_aws/picard_caller.rb, line 24 def self.build_index(bam_file_sorted_duplicates, picard_tools, log_file, job_prefix, account) cmd = "qsub -o #{log_file} -e #{log_file}_index_errors -V -cwd -b y -hold_jid duplicates_#{job_prefix} -N index_#{job_prefix} -l h_vmem=14G #{account} \ java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{bam_file_sorted_duplicates} VALIDATION_STRINGENCY=LENIENT" end
converter = “java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/SamFormatConverter.jar I=WT_aligned_sorted_rg.bam O=tmp.sam VALIDATION_STRINGENCY=LENIENT”
# File lib/mutations_caller_pipeline_aws/picard_caller.rb, line 3 def self.convert(sam_file, bam_file, picard_tools, log_file, job_prefix, account) cmd = "qsub -o #{log_file} -e #{log_file}_conversion_errors -V -cwd -b y -hold_jid bwa_#{job_prefix} -N convert_#{job_prefix} -l h_vmem=14G #{account} \ java -Xmx6g -jar #{picard_tools}/SamFormatConverter.jar I=#{sam_file} O=#{bam_file} VALIDATION_STRINGENCY=LENIENT " end
mark_duplicates
= “java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/MarkDuplicates.jar I=WT_aligned_sorted_rg.bam O=marked_dublicates.bam M=dublicate.metrcis AS=true VALIDATION_STRINGENCY=LENIENT”
# File lib/mutations_caller_pipeline_aws/picard_caller.rb, line 17 def self.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates, duplicate_metrcis, picard_tools, log_file, job_prefix, account) cmd = "qsub -o #{log_file} -e #{log_file}_duplicates_errors -V -cwd -b y -hold_jid sort_#{job_prefix} -N duplicates_#{job_prefix} -l h_vmem=14G #{account} \ java -Xmx3g -jar #{picard_tools}/MarkDuplicates.jar I=#{bam_file_sorted} O=#{bam_file_sorted_duplicates} M=#{duplicate_metrcis} \ AS=true VALIDATION_STRINGENCY=LENIENT" end
rg_and_sorting
= “java -jar -Xmx3g ~/Downloads/picard-tools-1.56/picard-tools-1.56/AddOrReplaceReadGroups.jar I=WT_aligned.bam O=WT_aligned_sorted_rg.bam SO=coordinate ID=15 LB=nina_library PL=Illumina PU=ATCATC SM=My_test VALIDATION_STRINGENCY=LENIENT”
# File lib/mutations_caller_pipeline_aws/picard_caller.rb, line 9 def self.rg_and_sorting(bam_file, bam_file_sorted, picard_tools, library, index, sample_name, log_file, id, job_prefix, account) cmd = "qsub -o #{log_file} -e #{log_file}_rg_sorting_errors -V -cwd -b y -hold_jid convert_#{job_prefix} -N sort_#{job_prefix} -l h_vmem=14G #{account} \ java -Xmx6g -jar #{picard_tools}/AddOrReplaceReadGroups.jar I=#{bam_file} O=#{bam_file_sorted} SO=coordinate ID=#{id} \ LB=#{library} PL=Illumina PU=#{index} SM=#{sample_name} VALIDATION_STRINGENCY=LENIENT MAX_RECORDS_IN_RAM=1500000" end