Changeset 5846

Timestamp:

Feb 26, 2020, 2:44:27 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1218: Implement MIPs alignment

Fixed some comments.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• config/reggie-config.xml (modified) (3 diffs)
• resources/mipsanalysis/align_start.jsp (modified) (2 diffs)

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

@@ -347 +347 @@
         </trimmomatic>
         
+        <!-- The amplicons BED files are used by novoalign -->
+        <!-- The main-dir setting should point to a directory with the BED files -->
+        <!-- Which BED file to use is determined by matching the 'panel' attribute with -->
+        <!-- the MIPS_Panel annotation from the DNA item. If no match is found the -->
+        <!-- alignment will fail. -->
         <amplicons>
           <main-dir>${ReferenceDir}/project/brcalab/b37/mipcombo_v0</main-dir>
@@ -356 +361 @@
         </amplicons>
         
+        <!-- Parameters that are needed by novoalign -->
         <novoalign>
           <index>${ReferenceDir}/novoalign/human_g1k_v37_decoy_dbSNP137_12M_k14s2.novoindex</index>
@@ -361 +367 @@
         </novoalign>
         
+        <!-- The following genome references are needed to extract some metrics after the alignment -->
         <genome-dict>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.dict</genome-dict>
         <genome-fasta>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.fasta</genome-fasta>
         
+        <!-- Options for the picard UmiAwareMarkDuplicatesWithMateCigar step -->
         <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>
+
+        <!-- Options for the picard CollectTargetedPcrMetrics step -->
         <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>

extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/align_start.jsp

@@ -109 +109 @@
           </td>
           <td class="help">
-            This step uses XXX for for aligning sequences. After the alignment
-            it will run YYYY as well
-            as a few other tools for statistics. Parameters are configured in 
-            &lt;align-mips&gt; section in reggie-config.xml.
+            This step uses novoalign for for aligning sequences. Parameters are 
+            configured in &lt;align-mips&gt; section in reggie-config.xml.
           </td>
         </tr>
@@ -148 +146 @@
             <span id="autoConfirm.message" class="message"></span>
             TODO -- 
-            If the alignment is successful and aligned pairs &gt;1M it is automatically confirmed
-            and StringTie is started. If aligned pairs is &lt;5M the RNA is flagged.
+            If the alignment is successful the next step is automatically
+            started. 
           </td>
         </tr>