From cee0b619373294718727a34ce358febbdea2f4b7 Mon Sep 17 00:00:00 2001 From: jwala Date: Mon, 15 May 2023 13:10:04 -0400 Subject: [PATCH] deprecated refilter and updated verison number --- README.md | 10 +++------- src/svaba/run_svaba.h | 2 +- src/svaba/svaba.cpp | 8 +++----- 3 files changed, 7 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index afc7dcb..790a715 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Table of contents * [Installation](#gh-md-toc) * [Description](#description) * [Output file description](#output-file-description) - * [Filtering and refiltering](#filtering-and-refiltering) + * [Filtering](#filtering-and-refiltering) * [Recipes and examples](#recipes-and-examples) * [Whole genome somatic SV and indel detection](#whole-genome-somatic-sv-and-indel-detection) * [Whole genome germline SV and indel detection](#whole-genome-germline-sv-and-indel-detection) @@ -75,8 +75,7 @@ Output file description ----------------------- ##### ``*.bps.txt.gz`` -Raw, unfiltered variants. This file is parsed at the end to produce the VCF files. With the bps.txt.gz, -one can define a new set of filteirng criteria (depending on sensitivity/specificity needs) using ``svaba refilter``. +Raw, unfiltered variants. This file is parsed at the end to produce the VCF files. ##### ``*.contigs.bam`` All assembly contigs as aligned to the reference with BWA-MEM. Note that this is an unsorted file. To view in IGV, @@ -105,7 +104,7 @@ the cutoff for rearrangement vs indel is taken from BWA-MEM, whether it produces or two separate alignments. This is an arbitrary cutoff, just as there is no clear consensus distinction between what constitutes an "indel" and a "structural variant". The unfiltered VCF files include non-PASS variants. -Filtering and Refiltering +Filtering ----------------------- SvABA performs a series of log-likelihood calculations for each variant. The purpose is to first classify a variant as real vs artifact, @@ -114,9 +113,6 @@ and then to determine if the variant is somatic or germline. These log-likelihoo * ``LR`` - Log of the odds that the variant has allelic fraction (AF) of 0 or >=0.5. This is used for somatic vs germline classification * ``SL`` - Scaled LOD. LOD scores is heuristically scaled as: (min(Mapping quality #1, Mapping quality #2) - 2 * NM) / 60 * LOD -SvABA can refilter the bps.txt.gz file to produce new VCFs with different stringency cutoffs. To run, the following are required: -* ``-b`` - a BAM from the original run, which is used just for its header -* ``-i`` - input bps.txt.gz file Examples and recipes -------------------- diff --git a/src/svaba/run_svaba.h b/src/svaba/run_svaba.h index 52ea3a5..7ffb917 100644 --- a/src/svaba/run_svaba.h +++ b/src/svaba/run_svaba.h @@ -24,7 +24,7 @@ #include "workqueue.h" -#define SVABA_VERSION "1.1.3" +#define SVABA_VERSION "1.2.0" // typedefs typedef std::map BamMap; diff --git a/src/svaba/svaba.cpp b/src/svaba/svaba.cpp index 5be0acc..e2a338e 100644 --- a/src/svaba/svaba.cpp +++ b/src/svaba/svaba.cpp @@ -24,7 +24,6 @@ static const char *SVABA_USAGE_MESSAGE = "Usage: svaba [options]\n\n" "Commands:\n" " run Run SvABA SV and Indel detection on BAM(s)\n" -" refilter Refilter the SvABA breakpoints with additional/different criteria to created filtered VCF and breakpoints file.\n" "\nReport bugs to jwala@broadinstitute.org \n\n"; int main(int argc, char** argv) { @@ -39,10 +38,9 @@ int main(int argc, char** argv) { return 0; } else if (command == "run") { runsvaba(argc -1, argv + 1); - } else if (command == "refilter") { - runRefilterBreakpoints(argc-1, argv+1); - } - else { + /* } else if (command == "refilter") { + runRefilterBreakpoints(argc-1, argv+1); */ + } else { std::cerr << SVABA_USAGE_MESSAGE; return 0; }