FindRepeatsPacBio

Introduction

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

Example

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.

Output

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