Which cloumn to take from SV Detect to make bed format to make it running on BEdtools

[vishal.rossi]

Bedtools intersect requires Bed format (chr name, starting and ending co-ordinate) for comparing two files. I have the file from svdetect but I don't know which column to extract for starting and ending co-ordinate.
Attaching the screenshot of output (can't capture all the columns).


>> SVDetect links2SV -conf <configuration_file>

This program converts the link list of the "<mates_file>.links.filtered" to show significant SVs through a
tabulated-text format. The output file name is "<mates_file>.links.filtered.sv.txt"

Each line corresponds to one chromosomal SV and the format is as follows:

1. Type of chromosomal rearrangement
Values:
INTRA: intra-chromosomal SV
INTER: inter-chromosomal SV

2. Predicted type of SV. See description in 2.b
3. Coordinates of chromosome1, format: chromosome:start-end
4. The mean separation distance is provided here if links have been filtered according to the insert size
5. Balanced or unbalanced feature. See description in 2.b
6. Coordinates of chromosome2, format: chromosome:start-end
7. Number of pairs after filtering
8. % of the remaining pairs after strand filtering
9. % of the remaining pairs after order filtering
10. % of the remaining pairs after insert size filtering
11. score based on 8., 9. and 10. (best score=1)
12. Coordinates of the estimated breakpoint region in chromosome1
13.Coordinates of the estimated breakpoint region in chromosome2

[syfo]

mhm... I think the description you posted does not match the format of the SV file.

Try something like

sed 1d mates_file.links.filtered.sv.txt | awk '$4==$7{OFS="\t";split($5,a,"-");split($8,b,"-");print $4,(a[1]<b[1]?a[1]:b[1]),(a[2]>b[2]?a[2]:b[2]),$2,$13*1000,"."}' > mates_file.links.filtered.sv.bed

The resulting bed file should be bedtools- and IGV- compatible.