Changeset 5830 for extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

Timestamp:

Feb 21, 2020, 11:35:42 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1218: Implement MIPs alignment

Added alignement with novoalign and merging of BAM files to a single BAM.

File:

• extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml (modified) (2 diffs)

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

@@ -202 +202 @@
           <path>/usr/local/packages/fgbio/0.8.1/fgbio.jar</path>
         </fgbio>
+        <novoalign>
+          <!-- full path to the novoalign file (required) -->
+          <path>/usr/local/packages/novocraft/V4.00.Pre-20190904/novoalign</path>
+        </novoalign>
+        <novosort>
+          <!-- full path to the novosort file (required) -->
+          <path>/usr/local/packages/novocraft/V4.00.Pre-20190904/novosort</path>
+        </novosort>
       </programs>
       
@@ -339 +347 @@
         </trimmomatic>
         
+        <amplicons>
+          <main-dir>${ReferenceDir}/project/brcalab/b37/mipcombo_v0</main-dir>
+          <bed panel="MI.B1B2.1">MIPCOMBO_B1B2_CHEK2_snpid55_snpid9plus_v01.bed</bed>
+          <bed panel="MI.ID.1">MIPCOMBO_CHEK2_snpid55_snpid9plus_v01.bed</bed>
+          <bed panel="MI.PALB2.1">MIPCOMBO_PALB2_CHEK2_snpid55_snpid9plus_v01.bed</bed>
+          <bed panel="MI.CDKN2A.1">MIPCOMBO_CDKN2A_CDK4_ex2_snpid55_snpid9plus_v01.bed</bed>
+          <bed panel="MI.TP53.1">MIPCOMBO_TP53_CHEK2_snpid55_snpid9plus_v01.bed</bed>
+        </amplicons>
+        
+        <novoalign>
+          <index>${ReferenceDir}/novoalign/human_g1k_v37_decoy_dbSNP137_12M_k14s2.novoindex</index>
+          <options>-o BAM 5 -o Sync -g 40 -x 1 --matchReward 4 --softclip 50,30 --trim3hp AG -H 22 -t 0,2.0 --hlimit 8 -v 150 -r R --Q2Off --pechimera off -F BAMPE RX</options>
+        </novoalign>
         
       </align-mips>