Tips Shim
From Crop Genomics Lab.
Revision as of 11:23, 8 April 2014 by Sangrea Shim (Talk | contribs)
about PiCard and GATK pipe for bam created by bwa aln pipe
java -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 like "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
