Tips Shim

about PiCard and GATK pipe for bam created by bwa aln pipe

  java -Djava.io.tmpdir=./temporary_dir/ -Xmx1g -jar /data/program/picard-tools-1.88/MarkDuplicates.jar\
  MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 METRICS_FILE=out.metrics REMOVE_DUPLICATES=true\
  ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT\
  INPUT=??.sorted.bam OUTPUT=??.sorted.bam.dedup.bam

• in higher version of PiCard, following error will occur. "bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned"

• using LINIENT option for VALIDATION_STRINGENCY will report "MAPQ should be 0 for unmapped read"

  swbarnes2 had explained about this problem at SeqAnswers

• If you want to do InDel realign, you have to run AddOrReplaceReadGroups.jar

• missing "-Djava.io.tmpdir=./temporary_dir/" options, make critical error and stop running as Yang Jae Kang mentioned in Tips kang.

altered reference sequence

• See this page

soft link

    $ ln -s (obj_file) (dir_for_link)

• useful when using personal module

Running same works with different combinations of argvs using GNU parallel

    $ parallel command {1} {2} ::: argv[1] ::: argv[2]

this command is the most efficient method to schedule large amount of iterative jobs. if you set the maximum core limitation, work threads retained as you set. one job ended, then another job will start. and total number of working threads will retained as constatnt.