SVseq2 Files

SVseq2 is a newer version of SVseq. 
This version takes BAM file with soft-clip signature as input.
This version is faster then SVseq.
This version has calls both deletions and insertions.

usage:

(1) Calling deletions:
./SVseq2 -r reference -b bam_file_list -c chr --o output_file[result.txt] --c cut_off[3] --is insert std

must have:
-r: the reference in fasta format
-b: list of BAM file names
-c: chromesome Name

optional:
--c cut off
--o out put file name
--is insert size and standard deviation (If provided, then all the files in the list has the same insert size and std; If not provided, SVseq2 tests the values for each file.)

(2) Calling insertions:
./SVseq2 -insertion -b bam_file_list -c chr --o output_file [result.txt] --ci cut_off[3]

must have:
-b: list of BAM file names
-c: chromesome Name

optional:
--ci cut off
--o out put file name