Possible to increase number of overlapping features returned?

[mmlian05]

Possible to increase number of overlapping features returned?

[lgmgeo]

Hi @mmlian05,

Thank you for your kind words :o)

Very large SV can sometime overlap too many features locations. It appears that depending on the visualisation program used (spreadsheet programs mostly) this annotation can be truncated. In order to avoid such embarrassing glitch and maybe also because overlapping so many features is already a problem, AnnotSV restricts the number of overlapping reported features.
Here are the features in question:

• RE_gene
• po_B_gain_someG_source
• po_B_gain_someG_coord
• po_B_loss_someG_source
• po_B_loss_someG_coord

If you want to change this behavior, you have to hack the code in 2 files:
(replace 19 or 49 by the desired maximum)

$ANNOTSV/share/tcl/AnnotSV/AnnotSV-benignsv.tcl:

lappend L_poBenignText($SVtoAnn) "[join [lrange $L_benign_source($SVtoAnn,$svtype,allG) 0 19] ";"]..."
lappend L_poBenignText($SVtoAnn) "[join [lrange $L_benign_coord($SVtoAnn,$svtype,allG) 0 19] ";"]..."
lappend L_poBenignText($SVtoAnn) "[join [lrange $L_benign_source($SVtoAnn,$svtype,someG) 0 19] ";"]..."
lappend L_poBenignText($SVtoAnn) "[join [lrange $L_benign_coord($SVtoAnn,$svtype,someG) 0 19] ";"]..."

$ANNOTSV/share/tcl/AnnotSV/AnnotSV-regulatoryelements.tcl:

set g_re($SV) "[join [lrange $g_re($SV) 0 49] ";"]..."

Best,
Véronique

[mmlian05]

Hi Véronique,

Thank you for the advice. Will try them out.

Wondering for user's own annotation should i look into the following *.tcl and line to modify the code?

$ANNOTSV/share/tcl/AnnotSV/AnnotSV-userBED.tcl:

set L_userBEDAnn_${i}($SVtoAnn) [lrange [set L_userBEDAnn_${i}($SVtoAnn)] 0 50]

Thank you! :)

Best regards,
Michelle

[lgmgeo]

Wondering for user's own annotation should i look into the following *.tcl and line to modify the code?
$ANNOTSV/share/tcl/AnnotSV/AnnotSV-userBED.tcl

Absolutely, yes