SVseq Files

SVseq is a tool to call deletions with exact break points. 

To learn how to use the program:
1 copy the proper program from executable/ to demo/
2 follow demo/demo.txt
3 compare the results with /demo/result/

Samtools is needed for the caller utility.

The input files are of 3 categories:
(1) anchor.
With the format: chromosome\tleft_position\tstrand\n
0 for forward strand, 1 for reverse strand.
(2) fastq.
The unmapped reads. 
(3) BAM files. That contains pair with both ends mapped.

Note: 
This version set a threshold >=50 on deletion length. 
Currently only works with paired-end reads.
For the fastq file: If a read is from BAM files, make sure it is not the reverse complement.
The insert size is defined as the left point to left point of a pair in this version.


Contact

Jin Zhang
jinzhang@engr.uconn.edu 
http://www.engr.uconn.edu/~jiz08001