SVseq2 Files

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

SVseq2 takes BAM file with soft-clip signature as input, is faster then SVseq 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_0_1 fixed a issue in loading a FASTA format file. Previously at least one word of description is required and Only capital case is allowed. This updated version makes description optional, but still requires a identifier. 

Note that the mapping algorithm hasn't been modified yet. So this version will ignore some SVs having flaking regions in lower cases.