Ignore:
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:
1 edited

Legend:

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

    r5829 r5830  
    202202          <path>/usr/local/packages/fgbio/0.8.1/fgbio.jar</path>
    203203        </fgbio>
     204        <novoalign>
     205          <!-- full path to the novoalign file (required) -->
     206          <path>/usr/local/packages/novocraft/V4.00.Pre-20190904/novoalign</path>
     207        </novoalign>
     208        <novosort>
     209          <!-- full path to the novosort file (required) -->
     210          <path>/usr/local/packages/novocraft/V4.00.Pre-20190904/novosort</path>
     211        </novosort>
    204212      </programs>
    205213     
     
    339347        </trimmomatic>
    340348       
     349        <amplicons>
     350          <main-dir>${ReferenceDir}/project/brcalab/b37/mipcombo_v0</main-dir>
     351          <bed panel="MI.B1B2.1">MIPCOMBO_B1B2_CHEK2_snpid55_snpid9plus_v01.bed</bed>
     352          <bed panel="MI.ID.1">MIPCOMBO_CHEK2_snpid55_snpid9plus_v01.bed</bed>
     353          <bed panel="MI.PALB2.1">MIPCOMBO_PALB2_CHEK2_snpid55_snpid9plus_v01.bed</bed>
     354          <bed panel="MI.CDKN2A.1">MIPCOMBO_CDKN2A_CDK4_ex2_snpid55_snpid9plus_v01.bed</bed>
     355          <bed panel="MI.TP53.1">MIPCOMBO_TP53_CHEK2_snpid55_snpid9plus_v01.bed</bed>
     356        </amplicons>
     357       
     358        <novoalign>
     359          <index>${ReferenceDir}/novoalign/human_g1k_v37_decoy_dbSNP137_12M_k14s2.novoindex</index>
     360          <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>
     361        </novoalign>
    341362       
    342363      </align-mips>
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