This tool searches for and annotates repeat regions inside a BAM file. It intersect the regions provided in the bed file with the BAM file and extracts them. On the extracted regions samtools mpileup will be run and all insertions, deletions or substitutions will be counted on a per read basis


To get the help menu:

biopet 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:

biopet 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