Sniffles2 v2.0.2

This is a major update to Sniffles v2 which includes:

• Improved variant calling accuracy
• Improved performance also on multi threading
• New methods to enable family / population calling
• New methods to enable somatic / mosaic SV detection

Detection of allele imbalance

Multiple improvements including:
-) Genotype prediction
-) Report of strand biases per allele
-) Higher sensitivity on low supported alleles
-) Improved forced calling

Better support for sequence resolved calls

• Improved reporting of sequence resolved calls.
• Minor bug fixes.

Bug fixes and updates

• Changed SVlen for deletions (new VCF standard)
• Changed BND output
• Improvements on genotyping for forced calling

Population calling

• Added functionality to call multisample genotyped SVs VCF file by interacting with SURVIVOR.
• Bug fixes for reporting sequences and force calling
• Added new interface for clearer navigation.

Multiple bug fixes

Sniffles:

• Added sequence resolved calls.
• Changed -n parameter (-n -1) reports now all read names.

Parameter added

--report_seq : Reports the sequences of Indels in the VCF output
--min_homo_af: Adapt the threshold to infer a homozygous variant
--min_het_af: Adapt the threshold to infer a heterozygous variant
--Ivcf: Enabling Recalling/force calling given a VCF file.

Bug fixes

• Bugs corrected in genotype estimation
• BND flag

Preprint release

Fixes

• Avoid calling SV in N stretches of certain sizes .
• Included genome header in vcf and BND type support.

Smaller bug fixes

Fixes

• More constrained calling of InvDup.
• Increased sensitivity for small indels.

Extension

• Parameter introduced: --ignore_std disable the filtering based on std.

Smaller bug fixes

Fixes

• Seg. fault sometimes occurring at the end of the run
• Enhanced resolution for smaller indel in noisy regions
• Constrained calling of INVDUP

Extention

• Parameter introduced: Min segment length

Enhanced filtering for false positives

v1.0.3

Smaller change in alignment processing