Difference between revisions of "Tips Shim"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) |
Sangrea Shim (Talk | contribs) |
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* useful when using personal module | * useful when using personal module | ||
| − | '''Running same works with different combinations of argvs using GNU parallel''' | + | '''Running same works with different combinations of argvs using [http://www.gnu.org/software/parallel/man.html#example__working_as_xargs__n1__argument_appending GNU parallel]''' |
$ parallel command {1} {2} ::: argv[1] ::: argv[2] | $ parallel command {1} {2} ::: argv[1] ::: argv[2] | ||
this command is the most efficient method to schedule large amount of iterative jobs. | 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. | 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. | one job ended, then another job will start. and total number of working threads will retained as constatnt. | ||
Revision as of 08:20, 21 April 2014
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.
