biostars and vcfgatkeval

docs/JvarkitCentral.md

@@ -2,8 +2,8 @@ JVARKIT
 =======
 
 Author      : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France.
-Version     : 0ceae1f9f
-Compilation : 20230616160652
+Version     : 8a9a881bc
+Compilation : 20230623173135
 Github      : https://github.com/lindenb/jvarkit
 Issues      : https://github.com/lindenb/jvarkit/issues
 

docs/SamJdk.md

@@ -113,6 +113,7 @@ Usage: samjdk [options] Files
  * [https://www.biostars.org/p/9524098](https://www.biostars.org/p/9524098)
  * [https://www.biostars.org/p/9532167](https://www.biostars.org/p/9532167)
  * [https://www.biostars.org/p/9537698](https://www.biostars.org/p/9537698)
+ * [https://www.biostars.org/p/9567318](https://www.biostars.org/p/9567318)
 
 
 

docs/VcfFilterJdk.md

@@ -119,6 +119,7 @@ Usage: vcffilterjdk [options] Files
  * [https://www.biostars.org/p/9527886](https://www.biostars.org/p/9527886)
  * [https://www.biostars.org/p/9536293](https://www.biostars.org/p/9536293)
  * [https://www.biostars.org/p/9537149](https://www.biostars.org/p/9537149)
+ * [https://www.biostars.org/p/9567314](https://www.biostars.org/p/9567314)
 
 
 

docs/VcfGatkEval.md

@@ -16,6 +16,9 @@ Usage: java -jar dist/jvarkit.jar vcfgatkeval  [options] Files
 
 Usage: vcfgatkeval [options] Files
   Options:
+    --depth
+      include INFO/DP
+      Default: false
     -h, --help
       print help and exit
     --helpFormat
@@ -137,6 +140,13 @@ ReadPosRankSum_HIGH_SNP
 SOR_HIGH_SNP
 ```
 
+use with gatk variantFilteration:
+
+```
+gatk VariantFiltration -V in.vcf.gz -R reference.fasta -O out.vcf.gz --arguments_file out1.output.filters.txt
+
+```
+
 # Parallelisation
 
 run in parallel

docs/index.md

@@ -2,8 +2,8 @@ JVARKIT
 =======
 
 Author      : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France.
-Version     : 0ceae1f9f
-Compilation : 20230616160652
+Version     : 8a9a881bc
+Compilation : 20230623173135
 Github      : https://github.com/lindenb/jvarkit
 Issues      : https://github.com/lindenb/jvarkit/issues
 
@@ -172,7 +172,7 @@ Please, read [how to run and install jvarkit](JvarkitCentral.md)
 | [sortvcfoninfo](SortVcfOnInfo.md) | Sort a VCF a field in the INFO column | 20140218 | 20201204 |
 | [sv2fasta](StructuralVariantToFasta.md) | convert VCF of structural variant(s) to fasta for pggb | 20230403 | 20230403 |
 | [vcfconcat](VcfConcat.md) | Concatenate VCFs with same sample. See also bcftools concat | 20131230 | 20230614 |
-| [vcfgatkeval](VcfGatkEval.md) | Eval/Plot gatk INFO tags for filtering | 20230424 | 20230425 |
+| [vcfgatkeval](VcfGatkEval.md) | Eval/Plot gatk INFO tags for filtering | 20230424 | 20230623 |
 | [vcfserver](VcfServer.md) | Web Server displaying VCF file. A web interface for vcf2table | 20171027 | 20220517 |
 | [vcfspliceai](VcfSpliceAI.md) | Annotate VCF with spiceai web service | 20201107 | 20201107 |
 | [vcftbi2bed](VcfTbiToBed.md) | extracts BED for each contig in a tabix-indexed VCF peeking first of last variant for each chromosome. | 20230214 | 20230214 |

src/main/java/com/github/lindenb/jvarkit/tools/samjs/SamJdk.java

@@ -384,7 +384,8 @@ public Object apply(final SAMRecord record) {
 		287057,299673,301080,305526,306034,309143,327317,335998,
                 336965,340479,342675,345679,362298,368754,378205,
                 408279,417123,427976,424431,450160,9464312,9489815,9493510,9498170,9511167,9524098,9532167,
-                9537698},
+                9537698,9567318
+		},
 	references="\"bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files\" . Bioinformatics, 2017. Pierre Lindenbaum & Richard Redon  [https://doi.org/10.1093/bioinformatics/btx734](https://doi.org/10.1093/bioinformatics/btx734).",
 	creationDate="20170807",
 	modificationDate="20191119",

src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java

@@ -419,7 +419,7 @@ public Object apply(final VariantContext V) {
 				304979,310155,317388,319148,327035,337645,343569,
 				347173,351205,351404,354126,302217,384864,416955,
 				436412,476718,9481318,9489144,9498113,9500825,9509515,9527886,9536293,
-				9537149
+				9537149,9567314
 				},
 		references="\"bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files\" . Bioinformatics, 2017. Pierre Lindenbaum & Richard Redon  [https://doi.org/10.1093/bioinformatics/btx734](https://doi.org/10.1093/bioinformatics/btx734).",
 		creationDate="20170705",

src/main/java/com/github/lindenb/jvarkit/tools/vcfgatkeval/VcfGatkEval.java

@@ -45,6 +45,7 @@ of this software and associated documentation files (the "Software"), to deal
 
 import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import htsjdk.variant.vcf.VCFIterator;
@@ -116,6 +117,13 @@ of this software and associated documentation files (the "Software"), to deal
 SOR_HIGH_SNP
 ```
 
+use with gatk variantFilteration:
+
+```
+gatk VariantFiltration -V in.vcf.gz -R reference.fasta -O out.vcf.gz --arguments_file out1.output.filters.txt
+
+```
+
 # Parallelisation
 
 run in parallel
@@ -140,7 +148,7 @@ of this software and associated documentation files (the "Software"), to deal
 		jvarkit_amalgamion = true,
 		keywords={"vcf","gatk"},
 		creationDate ="20230424",
-		modificationDate="20230425"
+		modificationDate="20230623"
 		)
 public class VcfGatkEval extends Launcher {
 	private static Logger LOG=Logger.build(VcfGatkEval.class).make();
@@ -152,6 +160,8 @@ private enum INPUT_TYPE{vcf,table};
 	private INPUT_TYPE inputType = INPUT_TYPE.vcf;
 	@Parameter(names={"-p","--percentile"},description="GATK Filters should be applied to this percentile: f < x < (1.0 -f)")
 	private double percentile= 0.025;
+	@Parameter(names={"--depth"},description="include INFO/" + VCFConstants.DEPTH_KEY)
+	private boolean include_depth = false;
 
 
 		private static class Range {
@@ -257,21 +267,22 @@ void saveFilter(PrintWriter out) throws IOException {
 				if(this.ranges.isEmpty()) return ;
 				final String testType;
 				switch(this.variantType) {
-					case SNP: testType = "vc.isSNP() && "; break;
-					case INDEL: testType = "vc.isIndel() && "; break;
+					case SNP: testType = "vc.isSNP()&&"; break;//no blank or gatk fails
+					case INDEL: testType = "vc.isIndel()&&"; break;//no blank or gatk fails
 					default: testType = ""; break;
 					}
+				final String hasAttribute = "vc.hasAttribute(\""+getTag()+"\")&&";
 				OptionalDouble limit = getLowPercentile();
 				if(limit.isPresent()) {
-					out.println("-filter");
-					out.println("\"" +testType + getTag() +" < "+ limit.getAsDouble()+ "\"");
+					out.println("--filter-expression");
+					out.println(testType + hasAttribute +  getTag() +"<"+ limit.getAsDouble()); //no blank or gatk fails
 					out.println("--filter-name");
 					out.println(getTag()+"_LOW_"+variantType.name());
 					}
 				limit = getHighPercentile();
 				if(limit.isPresent()) {
-					out.println("-filter");
-					out.println("\""+testType + getTag() +" > "+ limit.getAsDouble()+ "\"");
+					out.println("--filter-expression");
+					out.println(testType + hasAttribute + getTag() +">"+ limit.getAsDouble());//no blank or gatk fails
 					out.println("--filter-name");
 					out.println(getTag()+"_HIGH_"+variantType.name());
 					}
@@ -427,6 +438,13 @@ private class  MappingQualityRankSumTestAnnotation extends Annotation {
 
 		}
 
+		private class  DepthAnnotation extends Annotation {
+			DepthAnnotation(VariantContext.Type t) { super(t);}
+			@Override String getTag() { return VCFConstants.DEPTH_KEY;}
+			@Override int getPrecision() { return 1;}
+			@Override String getSub() {return "Depth";}
+		}
+
 		private class  ReadPosRankSumTestAnnotation extends Annotation {
 			ReadPosRankSumTestAnnotation(VariantContext.Type t) { super(t);}
 			@Override String getTag() { return "ReadPosRankSum";}
@@ -451,6 +469,9 @@ public int doWork(List<String> args) {
 				annotations.add(new RMSMappingQualityAnnotation(type));
 				annotations.add(new MappingQualityRankSumTestAnnotation(type));
 				annotations.add(new ReadPosRankSumTestAnnotation(type));
+				if(this.include_depth) {
+					annotations.add(new DepthAnnotation(type));
+					}
 				}
 			Collections.sort(annotations, (A,B)->{
 				int i= A.getTag().compareTo(B.getTag());