Changeset 5841 for extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

Timestamp:

Feb 25, 2020, 11:47:30 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1218: Implement MIPs alignment

Finalizing the MIPs alignment script by implementing the last two steps for collecting metrics. Results files are copied back to the project archive and linked in BASE to the alignment item.

Still need to implement importing some numbers as annotations from the metrics data.

File:

• extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml (modified) (1 diff)

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

@@ -364 +364 @@
         <genome-fasta>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.fasta</genome-fasta>
         
-        <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>
-        
+        <mark-duplicates-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-duplicates-options>
+        <pcr-metrics-options>-METRIC_ACCUMULATION_LEVEL null -METRIC_ACCUMULATION_LEVEL ALL_READS -MINIMUM_MAPPING_QUALITY 1 -MINIMUM_BASE_QUALITY 20 -CLIP_OVERLAPPING_READS true -COVERAGE_CAP 500 -NEAR_DISTANCE 5</pcr-metrics-options>
       </align-mips>