Module Detail Information

Name:Collect Alignment Summary Metrics
Type: Module
Short URL:
http://bit.ly/1C54Stu
Description:Read SAM and perform various fix-ups. Currently, the only fix-up it to soft-clip an alignment that hangs off the end of its reference sequence.
Executable:
/java
Input Parameters:
 - Jar File
 - Temp Location
 - Verbosity
 - Quiet
 - Validation Stringency
 - Compression Level
 - Max Records in RAM
 - Create Index
 - Create MD5 File
 - Input
 - Max Insert Size
 - Adapter Sequence
 - Is Bisulfite Sequenced
 - Reference Sequence
 - Don't Assume Sorted
 - Stop After
Output Parameters:
 - Output
File size:15.6 KB
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