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feat: External BED annotation files can now also be used to report an…
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…y feature overlapped with the SV (even with 1bp overlap) (v3.0.8)

External BED annotation files should be copied in:
- "$ANNOTSV/share/AnnotSV/Annotations_Human/Users/GRCh3*/FtIncludedInSV” directory
or
- "$ANNOTSV/share/AnnotSV/Annotations_Human/Users/GRCh3*/SVincludedInFt" directory
or
- "$ANNOTSV/share/AnnotSV/Annotations_Human/Users/GRCh3*/AnyOverlap" directory
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@lgmgeo
lgmgeo committed Jun 8, 2021
1 parent aee2e86 commit 38b22e9
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4 changes: 2 additions & 2 deletions Makefile
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
Expand Down Expand Up @@ -37,7 +37,7 @@ TCLVERSION := tcl$(shell echo 'puts $${tcl_version};exit 0' | tclsh)
TCLDIRDISTRIBUTED := share/tcl
TCLDIR := $(SHAREDIR)/$(TCLVERSION)
ANNOTSV := AnnotSV
VERSION := 3.0.7
VERSION := 3.0.8
RM := /bin/rm
RMDIR := /bin/rmdir
MKDIR := install -d
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#!/usr/bin/env tclsh

############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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3 changes: 2 additions & 1 deletion changeLog.txt
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# An integrated tool for Structural Variations annotation #
# #
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For more details, please see the README file.

- feat: External BED annotation files can now also be used to report any feature overlapped with the SV (even with 1bp overlap)
- feat: (i) Add the scoring points and (ii) remove gene names redundancy in the "AnnotSV_ranking_criteria" output column
- feat: Add bugfix concerning the use of the "candidateGenesFiltering" option
- feat: Include "NA" in the rankFiltering default option (default = "1-5,NA")
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2 changes: 1 addition & 1 deletion share/tcl/AnnotSV/AnnotSV-benignsv.tcl
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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2 changes: 1 addition & 1 deletion share/tcl/AnnotSV/AnnotSV-config.tcl
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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2 changes: 1 addition & 1 deletion share/tcl/AnnotSV/AnnotSV-cosmic.tcl
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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2 changes: 1 addition & 1 deletion share/tcl/AnnotSV/AnnotSV-encodeblacklist.tcl
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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2 changes: 1 addition & 1 deletion share/tcl/AnnotSV/AnnotSV-exac.tcl
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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############################################################################################################
# AnnotSV 3.0.7 #
# AnnotSV 3.0.8 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
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