This tool looks and annotates repeat regions inside a BAM file. It extracts the regions of interest from a bed file and then intersects those regions with the BAM file. On those extracted regions the tool will perform a Mpileup and counts all insertions/deletions etc. etc. for that specific location on a per read basis.


To get the help menu:

java -jar Biopet-0.2.0.jar tool FindRepeatsPacBio -h
Usage: FindRepeatsPacBio [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <file> | --inputBam <file>

  -b <file> | --inputBed <file>
        output file, default to stdout

To run the tool:

java -jar Biopet-0.2.0.jar tool FindRepeatsPacBio --inputBam myInputbam.bam \
--inputBed myRepeatRegions.bed > mySummary.txt

Since the default output of the program is printed in stdout we can use > to write the output to a text file.


The Output is a tab delimited text file which looks like this:

chr startPos stopPos Repeat_seq repeatLength original_Repeat_readLength
chr4 3076603 3076667 CAG 3 65
chr4 3076665 3076667 GCC 3 3
chrX 66765158 66765261 GCA 3 104

table continues below:

Calculated_repeat_readLength minLength maxLength inserts
61,73,68 61 73 GAC,G,T/A,C,G,G,A,G,A,G/C,C,C,A,C,A,G
3,3,3 3 3 //
98 98 98 A,G,G

table continues below:

deletions notSpan
1,1,2,1,1,1,2//2,1,1 0
// 0
1,1,1,1,1,1,2,1 0