improve clinCNV parameters for WGS somatic calling, call dragen CNVs only for WGS samples (no panel of normals made for WES yet)

Ott-Alexander · Ott-Alexander · commit 3793221ce1b9 · 2025-03-27T09:59:39.000+01:00
diff --git a/src/Pipelines/somatic_dna.php b/src/Pipelines/somatic_dna.php
@@ -457,8 +457,10 @@ function($str) { return explode("\t", $str); },
 		$args[] = "--log ".$dragen_log_file;
 		
 		$dragen_normal_vcf = $n_folder."/dragen_variant_calls/{$n_id}_dragen.vcf.gz";
-		if (is_file($dragen_normal_vcf))
+		
+		if ($sys['type'] == "WGS" && is_file($dragen_normal_vcf))
 		{
+			//calc dragen CNVs for WGS samples to compare results to clincnv
 			$args[] = "-out_cnv ".$dragen_output_cnvs;
 			$args[] = "-normal_snvs ".$dragen_normal_vcf;
 		}
@@ -1032,7 +1034,7 @@ function($str) { return explode("\t", $str); },
 			if($sys['type'] == "WGS")
 			{
 				$args_clincnv[] = "-lengthS 9";
-				$args_clincnv[] = "-scoreS 10000";
+				$args_clincnv[] = "-scoreS 1500";
 				$args_clincnv[] = "-filterStep 2";
 				$args_clincnv[] = "-clonePenalty 10000";
 			}

Original file line number	Diff line number	Diff line change
`@@ -457,8 +457,10 @@ function($str) { return explode("\t", $str); },`
`457`	`457`	`$args[] = "--log ".$dragen_log_file;`
`458`	`458`
`459`	`459`	`$dragen_normal_vcf = $n_folder."/dragen_variant_calls/{$n_id}_dragen.vcf.gz";`
`460`		`- if (is_file($dragen_normal_vcf))`
	`460`	`+`
	`461`	`+ if ($sys['type'] == "WGS" && is_file($dragen_normal_vcf))`
`461`	`462`	`{`
	`463`	`+ //calc dragen CNVs for WGS samples to compare results to clincnv`
`462`	`464`	`$args[] = "-out_cnv ".$dragen_output_cnvs;`
`463`	`465`	`$args[] = "-normal_snvs ".$dragen_normal_vcf;`
`464`	`466`	`}`
`@@ -1032,7 +1034,7 @@ function($str) { return explode("\t", $str); },`
`1032`	`1034`	`if($sys['type'] == "WGS")`
`1033`	`1035`	`{`
`1034`	`1036`	`$args_clincnv[] = "-lengthS 9";`
`1035`		`- $args_clincnv[] = "-scoreS 10000";`
	`1037`	`+ $args_clincnv[] = "-scoreS 1500";`
`1036`	`1038`	`$args_clincnv[] = "-filterStep 2";`
`1037`	`1039`	`$args_clincnv[] = "-clonePenalty 10000";`
`1038`	`1040`	`}`