Module Detail Information

Name:Reorder Sam
Type: Module
Short URL:
Description:Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. Runs substantially faster if the input is an indexed BAM file.Version: 1.0
Input Parameters:
 - Tmp dir
 - Verbosity
 - Quiet
 - Validation stringency
 - Compression level
 - Max records in ram
 - Create index
 - Create md5 file
 - Jar File
 - Input
 - Reference File
 - Allow Incomplete Dict Concordance
 - Allow Contig Length Discordance
Output Parameters:
 - Output
File size:13.76 KB
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