docu update for release 2024_06

imgag · Jun 25, 2024 · 2757273 · 2757273
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diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ Alternatively, *ngs-bits* can be built from sources. Use git to clone the most r
 
     > git clone --recursive https://github.com/imgag/ngs-bits.git
 	> cd ngs-bits
-	> git checkout 2024_02
+	> git checkout 2024_06
 	> git submodule update --recursive --init
 
 Depending on your operating system, building instructions vary slightly:
@@ -77,6 +77,7 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 
 * [BamClipOverlap](doc/tools/BamClipOverlap.md) - (Soft-)Clips paired-end reads that overlap.
 * [BamDownsample](doc/tools/BamDownsample.md) - Downsamples a BAM file to the given percentage of reads.
+* [BamExtract](doc/tools/BamExtract.md) - Extract reads from BAM/CRAM by read name.
 * [BamFilter](doc/tools/BamFilter.md) - Filters a BAM file by multiple criteria.
 * [BamHighCoverage](doc/tools/BamHighCoverage.md) - Determines high-coverage regions in a BAM file.
 * [BamToFastq](doc/tools/BamToFastq.md) - Converts a coordinate-sorted BAM file to FASTQ files.
@@ -133,13 +134,16 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 * [VcfExtractSamples](doc/tools/VcfExtractSamples.md) - Extract one or several samples from a VCF file.
 * [VcfFilter](doc/tools/VcfFilter.md) - Filters a VCF based on the given criteria.
 * [VcfLeftNormalize](doc/tools/VcfLeftNormalize.md) - Normalizes all variants and shifts indels to the left in a VCF file.
+* [VcfMerge](doc/tools/VcfMerge.md) - Merges several VCF files into one VCF.
 * [VcfSort](doc/tools/VcfSort.md) - Sorts variant lists according to chromosomal position.
+* [VcfSplit](doc/tools/VcfSplit.md) - Splits a VCF into several chunks.
 * [VcfStreamSort](doc/tools/VcfStreamSort.md) - Sorts entries of a VCF file according to genomic position using a stream.
 * [VcfSubstract](doc/tools/VcfSubstract.md) - Substracts the variants in a VCF from a second VCF.
 * [VcfToBed](doc/tools/VcfToBedpe.md) - Converts a VCF file to a BED file.
 * [VcfToBedpe](doc/tools/VcfToBedpe.md) - Converts a VCF file containing structural variants to BEDPE format.
 * [VcfToTsv](doc/tools/VcfToTsv.md) - Converts a VCF file to a tab-separated text file.
 
+
 ### BEDPE tools (structural variants)
 
 * [BedpeAnnotateFromBed](doc/tools/BedpeAnnotateFromBed.md) - Annotates a BEDPE file with information from a BED file.
@@ -172,16 +176,22 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 
 ## ChangeLog
 
-Changes in release 2024_02:
-
-* new tools: NGSDExportIgvGeneTrack, VcfMerge, VcfSplit, BamExtract
-* removed tools: CnvHunter
-* NGSDSameSample: Added option '-include_merged'
-* VcfFilter: Added options '-remove_non_ref' and '-no_special_chr'
-* VcfCheck: Added check for main header line
-* VariantRanking: using NGSD annotations by default now, skipping mosaic variants now
-* SampleSimilarity: added parameter 'roi_hg38_wes_wgs'
-* VcfLeftNormalize: now skips invalid variants
+Changes in release 2024_06:
+
+* new tools: NGSDExportIgvGeneTrack
+* removed tools: TODO
+* BamFilter: added parameter for maximum insert size
+* NGSDAddVariantsGermline: now imports REs as well
+* NGSDExportSamples: new paramters `-only_with_small_variants` and `-add_lab_columns`. 
+* SampleGender: new parameter `-include_single_end_reads` for long-read data.
+* SampleSimilarity: new parameter `-include_single_end_reads` for long-read data.
+* SampleSimilarity: new parameter `-roi_hg38_wes_wgs` to make WES, WGS and lrGS results more comparable.
+* UpdHunter: new parameter `-out_informative` to write out a IGV track with informative variants.
+* VcfCalculatePRS: new parameter `-min_depth` and support for variants that are to be imputed independent of the sample genotype.
+* NGSD:
+	* added tables for somatic SVs: somatic_somatic_sv_callset, somatic_sv_deletion, somatic_sv_duplication, somatic_sv_insertion, somatic_sv_inversion, somatic_sv_translocation, somatic_report_configuration_sv
+	* added tables for repeat expansions: repeat_expansion, repeat_expansion_genotype, re_callset, report_configuration_re
+	* processed_sample table: added boolean `scheduled_for_resequencing` to flag samples for resequencing to increase depth/coverage
 
 
 For older changes see [releases](https://github.com/imgag/ngs-bits/releases).
diff --git a/doc/checklist_new_release.md b/doc/checklist_new_release.md
@@ -2,7 +2,7 @@
 
 1. Update documentation: `make build_release_noclean doc_update`
 1. Update check documentation: `make doc_check_urls`
-1. Check for tools not added to the main page: `makedoc_find_missing_tools`
+1. Check for tools not added to the main page: `make doc_find_missing_tools`
 1. Update the changelog in `ngs-bits/README.md`.
 
 	> git diff -w [last-tag] master src/cppNGSD/resources/NGSD_schema.sql  

diff --git a/doc/tools/NGSDAddVariantsSomatic.md b/doc/tools/NGSDAddVariantsSomatic.md
@@ -1,5 +1,5 @@
 ### NGSDAddVariantsSomatic tool help
-	NGSDAddVariantsSomatic (2019_09-51-g84b6c695)
+	NGSDAddVariantsSomatic (2024_02-126-g4f44d5e5)
 
 	Imports variants of a tumor-normal processed sample into the NGSD.
 
@@ -16,6 +16,10 @@
 	                 Default value: ''
 	  -cnv_force     Force import of CNVs, even if already imported.
 	                 Default value: 'false'
+	  -sv <file>     SV list in TSV format (as produced by megSAP).
+	                 Default value: ''
+	  -sv_force      Force import of SVs, even if already imported.
+	                 Default value: 'false'
 	  -out <file>    Output file. If unset, writes to STDOUT.
 	                 Default value: ''
 	  -test          Uses the test database instead of on the production database.
@@ -32,6 +36,6 @@
 	  --tdx          Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### NGSDAddVariantsSomatic changelog
-	NGSDAddVariantsSomatic 2019_09-51-g84b6c695
+	NGSDAddVariantsSomatic 2024_02-126-g4f44d5e5
 
 [back to ngs-bits](https://github.com/imgag/ngs-bits)
diff --git a/doc/tools/NGSDExportIgvGeneTrack.md b/doc/tools/NGSDExportIgvGeneTrack.md
@@ -1,13 +1,13 @@
 ### NGSDExportIgvGeneTrack tool help
-	NGSDExportIgvGeneTrack (2023_11-133-g87eceb58)
+	NGSDExportIgvGeneTrack (2024_02-126-g4f44d5e5)
 
 	Writes all transcripts and exons of all genes to a IGV-readable text file.
 
 	Mandatory parameters:
 	  -out <file>      The output text file.
 
 	Optional parameters:
-	  -out_mane <file> The optional output text file containing only MANE + clinical transcripts.
+	  -out_mane <file> The optional output text file containing only MANE transcripts.
 	                   Default value: ''
 	  -test            Uses the test database instead of on the production database.
 	                   Default value: 'false'
@@ -19,6 +19,6 @@
 	  --tdx            Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### NGSDExportIgvGeneTrack changelog
-	NGSDExportIgvGeneTrack 2023_11-133-g87eceb58
+	NGSDExportIgvGeneTrack 2024_02-126-g4f44d5e5
 
 [back to ngs-bits](https://github.com/imgag/ngs-bits)
diff --git a/doc/tools/SvFilterAnnotations.md b/doc/tools/SvFilterAnnotations.md
@@ -1,5 +1,5 @@
 ### SvFilterAnnotations tool help
-	SvFilterAnnotations (2023_11-42-ga9d1687d)
+	SvFilterAnnotations (2024_02-126-g4f44d5e5)
 
 	Filter a structural variant list in BEDPE format based on variant annotations.
 
@@ -60,7 +60,7 @@
 	                            Parameters:
 	                              complete - Overlaps the complete gene. [default=true]
 	                              exonic/splicing - Overlaps the coding or splicing region of the gene. [default=true]
-	                              intronic/intergenic - Overlaps the intronic/intergenic region of the gene only. [default=false]
+	                              intronic/near gene - Overlaps the intronic region or less than 5kb up/down stream of the gene . [default=false]
 	SV genotype affected        Filter structural variants (of affected samples) based on their genotype.
 	                            Parameters:
 	                              genotypes - Structural variant genotype(s) [valid=wt,het,hom,n/a] [non-empty]
@@ -117,7 +117,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### SvFilterAnnotations changelog
-	SvFilterAnnotations 2023_11-42-ga9d1687d
+	SvFilterAnnotations 2024_02-126-g4f44d5e5
 
 	2020-04-16 Initial version of the tool. Based on VariantFilterAnnotations.
 [back to ngs-bits](https://github.com/imgag/ngs-bits)
diff --git a/doc/tools/VariantFilterAnnotations.md b/doc/tools/VariantFilterAnnotations.md
@@ -1,5 +1,5 @@
 ### VariantFilterAnnotations tool help
-	VariantFilterAnnotations (2024_02-42-g36bb2635)
+	VariantFilterAnnotations (2024_02-126-g4f44d5e5)
 
 	Filter a variant list in GSvar format based on variant annotations.
 
@@ -146,8 +146,8 @@
 	                                     build - Genome build used for pseudoautosomal region coordinates [default=hg38] [valid=hg19,hg38]
 	Tumor zygosity                     Filter based on the zygosity of tumor-only samples. Filters out germline het/hom calls.
 	                                   Parameters:
-	                                     het_af_range - Consider allele frequencies of 50% ± het_af_range as heterozygous and thus as germline. [default=0] [min=0] [max=49.9]
-	                                     hom_af_range - Consider allele frequencies of 100% ± hom_af_range as homozygous and thus as germline. [default=0] [min=0] [max=99.9]
+	                                     het_af_range - Consider allele frequencies of 50% ± het_af_range as heterozygous and thus as germline. [default=0] [min=0] [max=49.9]
+	                                     hom_af_range - Consider allele frequencies of 100% ± hom_af_range as homozygous and thus as germline. [default=0] [min=0] [max=99.9]
 	Variant quality                    Filter for variant quality
 	                                   Parameters:
 	                                     qual - Minimum variant quality score (Phred) [default=250] [min=0]
@@ -165,6 +165,9 @@
 	                                     MODERATE - Moderate impact variant types [default=inframe_deletion,inframe_insertion,missense_variant] [valid=inframe_deletion,inframe_insertion,missense_variant]
 	                                     LOW - Low impact variant types [default=splice_region_variant] [valid=splice_region_variant,stop_retained_variant,synonymous_variant]
 	                                     MODIFIER - Lowest impact variant types [valid=3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,downstream_gene_variant,intergenic_variant,intron_variant,mature_miRNA_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,upstream_gene_variant]
+	lr short-read overlap              Filter that preserves variants if they were called in short-read WGS sample only.
+	                                   Parameters:
+	                                     invert - If set, removes all variants if they were called in short-read WGS sample. [default=false]
 
 	Mandatory parameters:
 	  -in <file>      Input variant list in GSvar format.
@@ -178,7 +181,7 @@
 	  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### VariantFilterAnnotations changelog
-	VariantFilterAnnotations 2024_02-42-g36bb2635
+	VariantFilterAnnotations 2024_02-126-g4f44d5e5
 
 	2018-07-30 Replaced command-line parameters by INI file and added many new filters.
 	2017-06-14 Refactoring of genotype-based filters: now also supports multi-sample filtering of affected and control samples.

diff --git a/doc/tools/VcfCalculatePRS.md b/doc/tools/VcfCalculatePRS.md
@@ -1,5 +1,5 @@
 ### VcfCalculatePRS tool help
-	VcfCalculatePRS (2024_02-42-g36bb2635)
+	VcfCalculatePRS (2024_02-126-g4f44d5e5)
 
 	Calculates the Polgenic Risk Score(s) for a sample.
 
@@ -14,6 +14,8 @@
 	  -out <file>      Output TSV file containing Scores and PRS details
 
 	Optional parameters:
+	  -details <file>  Output TSV containing each variant with weight, allele count and population AF.
+	                   Default value: ''
 	  -ref <file>      Reference genome FASTA file. If unset, 'reference_genome' from the 'settings.ini' file is used.
 	                   Default value: ''
 	  -min_depth <int> Depth cutoff below which uncalled SNPs are considered not callable and POP_AF is used instead of genotype.
@@ -26,8 +28,10 @@
 	  --tdx            Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
 
 ### VcfCalculatePRS changelog
-	VcfCalculatePRS 2024_02-42-g36bb2635
+	VcfCalculatePRS 2024_02-126-g4f44d5e5
 
+	2024-06-05 Added support for imputed variants.
+	2024-04-22 Added output of factors and support for wt variants.
 	2022-12-15 Added BAM depth check and population AF.
 	2020-07-22 Initial version of this tool.
 [back to ngs-bits](https://github.com/imgag/ngs-bits)