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changeLog.txt
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############################################################################################################
# liftoverSV 0.1.2_beta #
# #
# Copyright (C) 2024-current Veronique Geoffroy ([email protected]) #
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License #
# as published by the Free Software Foundation; either version 3 #
# of the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; If not, see <http://www.gnu.org/licenses/>. #
############################################################################################################
For more details, please see the README file.
Jan, , 2025, liftoverSV version 0.1.3_beta
- Lift over REF and ALT (sequences + coordinates)
- Check if the VCF input file contains multi-allelic lines (not allowed)
- Check/Update INFO/CIPOS and INFO/CIEND
- Update/create and sort some VCF header lines
- Checks that the "contig" field includes all the ID attributes (do not include additional optional attributes)</br>
e.g. `##contig=<ID=chr22>` added after a lift from chr1 to chr22
- Create/update the "assembly" field
e.g. `##assembly=liftoverSV used with hg19ToHg38.over.chain`
- Create the "liftoverSV_version" field
e.g. `##liftoverSV_version=0.1.2_beta; hg19ToHg38.over.chain; August 30 2024 12:30`
- Update the "INFO" and "FORMAT field if one value is missing.
As the format (Number, String) is not known, "Number=." and "Type=String" values are used by default:
e.g. `##FORMAT=<ID=XXX,Number=.,Type=String,Description="XXX">`
e.g. `##INFO=<ID=YYY,Number=.,Type=String,Description="YYY">`
July, 23, 2024, liftoverSV version 0.1.2_beta
- Sort and compress the VCF output file with bcftools
- Display the number of mapped SV in the output
- Update the contig field in the VCF header output:
=> The structured contig field includes all the ID attributes (do not include additional optional attributes)
e.g. `##contig=<ID=chr22>`
- Add a DOI in README.md
- Lift over INFO/SVLEN, INFO/SVSIZE only for deletion, duplication, insertion and inversion
=> For other SV types (e.g. translocation, complex SV, etc..), the SVLEN is set to . in the output file when present in the input file
- Check if the VCF input file and the CHAIN file have the same chromosome format (with or without the "chr" prefix)
July, 23, 2024, liftoverSV version 0.1.1_beta
- Add the --PERCENT,P option
July, 12, 2024, liftoverSV version 0.1.0_beta
liftoverSV: Lifts over a Structural Variation VCF file from one reference build to another.
Purpose:
- Lift over #CHROM and POS
- Lift over INFO/END and INFO/SVEND
=> drop the SV if:
Case1: one position (start or end) is lifted while the other doesn't
Case2: one position (start or end) goes to a different chrom from the other
Case3: "lifted start" > "lifted end"
Case4: the distance between the two lifted positions changes significantly (difference between both SVLENs > 5%)
- Lift over INFO/SVLEN, INFO/SVSIZE