Module Detail Information

Name:Merge Bam Alignment
Type: Module
Short URL:
Description:Merges alignment data from a SAM or BAM file with additional data stored in an unmapped BAM file and produces a third SAM or BAM file of aligned and unaligned reads. NOTE that this program expects to find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it to have the same base name as the reference fasta except with the extension '.dict'
Input Parameters:
 - Tmp dir
 - Verbosity
 - Quiet
 - Validation stringency
 - Compression level
 - Max records in ram
 - Create index
 - Create md5 file
 - Jar File
 - Unmapped BAM
 - Aligned BAM
 - Read 1 Aligned BAM
 - Read 2 Aligned BAM
 - Reference Sequence
 - Program Record ID
 - Program Group Version
 - Program Group Command Line
 - Program Group Name
 - Paired Run
 - Don't Clip Adapters
 - Is Bisulfite Sequence
 - Aligned Reads Only
 - Max Insertions or Deletions
 - Attributes to Retain
 - Read 1 Trim
 - Read 2 Trim
 - Expected Orientations
Output Parameters:
 - Output
File size:22.13 KB
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