Ignore:
Timestamp:
Feb 21, 2020, 2:36:41 PM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1218: Implement MIPs alignment

Final steps in the alignment pipeline. Re-headers, splitting and marking duplicates. All critical work has been done. There are still some collections of metrics to implement, as well as error handling and storing result files back to the project archive.

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1 edited

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  • extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

    r5830 r5831  
    361361        </novoalign>
    362362       
     363        <genome-dict>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.dict</genome-dict>
     364        <genome-fasta>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.fasta</genome-fasta>
     365       
     366        <mark-duplicate-options>-CREATE_INDEX true -CREATE_MD5_FILE true -MAX_FILE_HANDLES 20000 -ALLOW_MISSING_UMIS false -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -MAX_EDIT_DISTANCE_TO_JOIN 1 -REMOVE_DUPLICATES true</mark-duplicate-options>
     367       
    363368      </align-mips>
    364369     
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