From eaed4d7bbad46ae4aebe8b21cc17470076f38a60 Mon Sep 17 00:00:00 2001 From: Chris Saunders Date: Fri, 4 Apr 2014 03:53:48 -0700 Subject: [PATCH] Lower default min candidate size to 8 --- ChangeLog.txt | 2 ++ src/markdown/mantaUserGuide.md | 4 ++-- src/python/bin/configManta.py.ini | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index c41266f8..82521924 100644 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,5 @@ +v0.20.1 +- Lower default min candidate size to 8 v0.20.0 - MANTA-136 turn on conservative large insertion calling - MANTA-126 multi-junction SV scoring diff --git a/src/markdown/mantaUserGuide.md b/src/markdown/mantaUserGuide.md index c8f84d25..59aa990b 100644 --- a/src/markdown/mantaUserGuide.md +++ b/src/markdown/mantaUserGuide.md @@ -72,7 +72,7 @@ levels and take other RNA-specific filtration and intron handling steps. Manta is able to detect all variation classes which can be explained as novel DNA adjacencies in the genome. Simple insertion/deletion events can be -detected down to a configurable minimum size cutoff (defaulting to 10). All DNA +detected down to a configurable minimum size cutoff (defaulting to 8). All DNA adjacencies are classified into the following categories based on the breakend pattern: @@ -157,7 +157,7 @@ is provided. These files are: evidence is required for a SV to be entered as a candidate. An SV or indel must be a candidate to be considered for scoring, therefore an SV cannot appear in the other VCF outputs if it is not present in this file. Note that - by default this file includes indels down to a very small size (>= 10 bases). + by default this file includes indels down to a very small size (>= 8 bases). These are intended to be passed on to a small variant caller without scoring by manta itself (by default manta scoring starts at size 51). * __diploidSV.vcf.gz__ diff --git a/src/python/bin/configManta.py.ini b/src/python/bin/configManta.py.ini index 35935ad7..0b5ed417 100644 --- a/src/python/bin/configManta.py.ini +++ b/src/python/bin/configManta.py.ini @@ -7,7 +7,7 @@ referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa # Run discovery and candidate reporting for all SVs/indels at or above this size: -minCandidateVariantSize = 7 +minCandidateVariantSize = 8 # After candidate identification, only score and report SVs/indels at or above this size: minScoredVariantSize = 51