SVseq2 Files

SVseq2 is a newer version of SVseq1. 
(Actually quite different in terms of the basic utilities. This version doesn't use BWT anymore, but uses focal regions in finding deletions. However, SVseq2 also uses pair-end information, which is similar to SVseq1.) 

SVseq2 takes BAM file with soft-clip signature as input, is faster then SVseq1 and is calling 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



For deletion calling, there is another option -nosplit2 which requires the program only use type I pattern.

SVseq2_2 ignores the repeats annotations (SVseq2_0_1 awares those) in the reads mapping step. In deed, some SVs can be caused by repeats. 

SVseq2_2 also fixes a bug. Prevoius, when a split read is partially mapped to the first chromosome at very a small coordinate, the focal region could be pointed to minus locations. This can cause a overflow and stops the program when the program performs other checkings.