Class: PicardCaller

Inherits:
Object
  • Object
show all
Defined in:
lib/mutations_caller_pipeline_aws/picard_caller.rb

Class Method Summary collapse

Class Method Details

.build_index(bam_file_sorted_duplicates, picard_tools, log_file, job_prefix, account) ⇒ Object

build_index = “java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/BuildBamIndex.jar I=marked_dublicates.bam VALIDATION_STRINGENCY=LENIENT”



24
25
26
27
 
# 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, )
  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 #{} \
    java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{bam_file_sorted_duplicates}  VALIDATION_STRINGENCY=LENIENT"
end

.convert(sam_file, bam_file, picard_tools, log_file, job_prefix, account) ⇒ Object

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”



3
4
5
6
 
# File 'lib/mutations_caller_pipeline_aws/picard_caller.rb', line 3

def self.convert(sam_file, bam_file, picard_tools, log_file, job_prefix, )
  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 #{} \
    java -Xmx6g -jar  #{picard_tools}/SamFormatConverter.jar I=#{sam_file} O=#{bam_file} VALIDATION_STRINGENCY=LENIENT "
end

.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates, duplicate_metrcis, picard_tools, log_file, job_prefix, account) ⇒ Object

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”



17
18
19
20
21
 
# 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, )
  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 #{} \
    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(bam_file, bam_file_sorted, picard_tools, library, index, sample_name, log_file, id, job_prefix, account) ⇒ Object

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”



9
10
11
12
13
 
# 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, )
  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 #{} \
    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