v1.5

Change Log: 12/16/2019

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• fixed bug in Merge.py.

v1.4.3.4

SV² v1.4.3.4

06/11/2018

commit 72ce91d

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Change Log

• Added option for user-defined config file (sv2.ini): thank you holtgrewe
• Fixed VCF header format: thank you holtgrewe

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❗ Please use the sv2-1.4.3.4.tar.gz link not the "Source Code" links. ❗

v1.4.3.3

SV² v1.4.3.3

04/28/2018

commit 155e2b5

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Change Log

• skips regions not present in SNV VCF: #8
• added -O, -odir option to define the path to output directories
• added python 2.7 install requirement (timothymillar): #5
• fixed bug in merging when chromosome prefixes do not start with "chr"

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❗ Please use the sv2-1.4.3.3.tar.gz link not the "Source Code" links. ❗

v1.4.1

SV² v1.4.1

03/08/2018

commit 9905c84

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Change Log

• uploaded package to pypi pip install sv2
• sv2 -download step to download required resource files

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❗ Please use the sv2-1.4.1.tar.gz link not the "Source Code" links. ❗

v1.4.0

SV² v1.4.0

02/28/2018

commit 813e36a

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Change Log

• supports CRAM files
• supports mm10 genotyping
• supports scikit-learn >= v0.19
• option to skip annotation -no-anno
• deobfuscated code, improved execution time
• simplified command line arguments
• removed need for sample information file, now pass the input files directly!
• uses sample identifier from the bam header
• uses reference lengths from the bam header
• standard error now outputs to a log file
• fixed bugs in filtering
• fixed errors in gene annotation
• heterozygous allele ratio supports multiallelic variants
• removed parallelization capabilities

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❗ Please use the sv2-1.4.0.tar.gz link not the "Source Code" links. ❗

Version 1.3.2

Change Log

• Added function to merge SV after genotyping
• Users can now retrain default models or train their own
• Users can supply both BED and VCF files at the same time sv2 -i in.txt [-b ...] [-v ...]

Ignore the notice about being behind in comments. Also do not download the "Source Code". The actual source package are sv2-1.3.2.tar.gz and sv2-1.3.2.zip

SV2 v1.3

This version of SV² now supports BAM files that have been aligned without the legacy option -M for bwa mem.

If the BAM file was aligned using the legacy -M flag, pass the -M flag to SV²

SV2v1.2

This version contains an improved classifier for genotyping deletions on male sex chromosomes.

The new release simplifies configuration.

The new release supports pip install

SV2v1.1

SV² version 1.1 with standard filters and stringent filters for de novo mutation discovery.

Source binaries:

• zip
• tar.gz