merge master changes to develop

Clinical-Genomics · Apr 4, 2022 · a80860c · a80860c
2 parents bd70c3a + 9578e97
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -17,6 +17,9 @@ tag_name = v{new_version}
 [bumpversion:file:docs/bioinfo_softwares.rst]
 
 [bumpversion:file:docs/user_guide.rst]
+
+[bumpversion:file:docs/install.rst]
+
 search = {current_version}
 replace = {new_version}
 
diff --git a/BALSAMIC/commands/init/base.py b/BALSAMIC/commands/init/base.py
@@ -126,7 +126,7 @@
 )
 @click.option(
     "--qos",
-    type=click.Choice(["low", "normal", "high"]),
+    type=click.Choice(["low", "normal", "high", "express"]),
     show_default=True,
     default="low",
     help="QOS for sbatch jobs. Passed to " + get_schedulerpy(),

diff --git a/BALSAMIC/commands/run/analysis.py b/BALSAMIC/commands/run/analysis.py
@@ -106,7 +106,7 @@
 )
 @click.option(
     "--qos",
-    type=click.Choice(["low", "normal", "high"]),
+    type=click.Choice(["low", "normal", "high", "express"]),
     show_default=True,
     default="low",
     help="QOS for sbatch jobs. Passed to " + get_schedulerpy(),

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,8 @@
 Added:
 ^^^^^^
 
+* Added slurm qos tag `express` #885
+* Included more text about UMI-workflow variant calling settings to the readthedocs #888
 * Snakemake workflow to create canfam3 reference #843
 * Call umi variants using TNscope in bed defined regions #821
 * UMI duplication metrics to report in multiqc_picard_dups.json #844
@@ -22,11 +24,11 @@ Changed:
 * Merge QC metric extraction workflows #833
 * Changed the base-image for balsamic container to 4.10.3-alpine #869
 * updated SVdb to 2.6.0 #871
-
+* Upgrade black to 22.3.0
 
 Fixed:
 ^^^^^^
-
+* Automate balsamic version for readthedocs install page #888
 * ``collect_qc_metrics.py`` failing for WGS cases with empty ``capture_kit`` argument #850
 * QC metric validation for different panel bed version #855
 
@@ -38,12 +40,12 @@ Removed
 * SV and CNV callers from annotation and filtering #871
 * vcfanno from SV annotation
 
+
 [8.2.8]
 --------
 
 Added:
 ^^^^^^
-
 * Added the readthedocs page for BALSAMIC variant-calling filters #867
 * Project requirements (setup.py) to build the docs #874 
 * Generate cram from umi-consensus called bam files #865

diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst
@@ -33,7 +33,6 @@ indicate that at this site, the mean position in reads is less than 8 and positi
 For `Post-call filtering`, in BALSAMIC we have applied various filtering criteria (`Vardict_filtering`_, `TNscope filtering (Tumor_normal)`_ ) depending on the analysis-type (TGS/WGS) and sample-type(tumor-only/tumor-normal).
 
 .. important::
-
     In BALSAMIC, this VCF file is named as `*.all.filtered.pass.vcf.gz` (eg: `SNV.somatic.<CASE_ID>.vardict.all.filtered.pass.vcf.gz`)
 
 **Targeted Genome Analysis**
@@ -80,7 +79,6 @@ Following are the set of criterias applied for filtering vardict results. Applie
     Maximum AF < 1
 
 .. attention::
-
     BALSAMIC <= v8.2.7 uses minimum AF 1% (0.01). From Balsamic v8.2.8, minimum VAF is changed to 0.7% (0.007)
 
 *GNOMADAF_POPMAX*: Maximum Allele Frequency across populations
@@ -90,7 +88,6 @@ Following are the set of criterias applied for filtering vardict results. Applie
     GNOMADAF_popmax <= 0.005  (or) GNOMADAF_popmax == "."
 
 .. important::
-
     Additionally, for tumor-normal cases; the variant is excluded if it marked as 'germline' in the `STATUS` column of vcf file.
 
 **Whole Genome Sequencing (WGS)**
@@ -187,6 +184,31 @@ The `TNscope <https://www.biorxiv.org/content/10.1101/250647v1.abstract>`_ algor
 `UMI workflow <https://balsamic.readthedocs.io/en/latest/FAQs.html>`_ performs the variant calling of SNVs/INDELS using the `TNscope` algorithm from UMI consensus-called reads.
 The following filter applies for both tumor-normal and tumor-only samples.
 
+**Pre-call Filters**
+
+*minreads*: Filtering of consensus called reads based on the minimum reads supporting each UMI tag group
+
+::
+
+    minreads = 3,1,1
+
+Which means that at least `3` UMI tag groups should be ideally considered from both DNA strands, where a minimum of atleast `1` UMI tag group should exist in each of the single-stranded consensus reads.
+
+*min_init_tumor_lod* : Log odds is the likelihood that the candidate mutation is real over the likelihood that the candidate mutation is a sequencing error before any read-based filters are applied.
+minimum log odds for the candidate selection. TNscope default: `4`
+
+::
+
+    min_init_tumor_lod = 0.5
+
+*min_tumor_lod* : minimum log odds in the final call of variants. TNscope default: `6.3`
+
+::
+
+    min_tumor_lod = 4.0
+
+**Post-call Filters**
+
 *GNOMADAF_POPMAX*: Maximum Allele Frequency across populations
 
 ::

diff --git a/docs/install.rst b/docs/install.rst
@@ -2,7 +2,7 @@
 Installation
 ============
 
-This section describes steps to install BALSAMIC (**version** = 4.1.0)
+This section describes steps to install BALSAMIC (**version** = 8.2.8)
 
 
 

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -2,6 +2,6 @@ pytest>=3.7.1
 pytest-cov==2.8.1
 coveralls
 pylint
-black==21.7b0
+black==22.3.0
 pillow>=8.4.0
 fpdf2>=2.4.6