Difference between revisions of "Tips Shim"
From Crop Genomics Lab.
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'''about PiCard and GATK pipe for bam created by bwa aln pipe''' | '''about PiCard and GATK pipe for bam created by bwa aln pipe''' | ||
| − | java -Xmx1g -jar /data/program/picard-tools-1.88/MarkDuplicates.jar\ | + | 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\ | MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 METRICS_FILE=out.metrics REMOVE_DUPLICATES=true\ | ||
ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT\ | ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT\ | ||
INPUT=??.sorted.bam OUTPUT=??.sorted.bam.dedup.bam | INPUT=??.sorted.bam OUTPUT=??.sorted.bam.dedup.bam | ||
| − | in higher version of PiCard, following error will occur | + | * 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" | + | * using LINIENT option for VALIDATION_STRINGENCY will report "MAPQ should be 0 for unmapped read" |
| + | [http://seqanswers.com/forums/showthread.php?t=11421 swbarnes2] had explained about this problem at [http://seqanswers.com/ 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]]. | ||
Revision as of 07:38, 11 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.
