Interpret FORMAT/SQ as Float (#93)

Closes: #93 Related-Issue: #93 Projected-Results-Impact: none
varfish-org · Jan 16, 2023 · 1940b1d · 1940b1d
1 parent f68d82e
commit 1940b1d
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Showing 3 changed files with 10 additions and 4 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,8 @@
 
 ## v0.31 (work in progress)
 
+- Interpret `FORMAT/SQ` as Float (#93).
+
 ## v0.30
 
 - Adding support for MELT (#91).
@@ -15,7 +17,7 @@
 - Write out `FORMAT/SQ` in the case that is present and `FORMAT/GQ` is not (#84).
   If neither is set, then write out `0`.
   Write out `0` for `AD` and `DP` as well if missing.
-  This improves compatibility with Manta.
+  This improves compatibility with DRAGEN.
 - Suppress BND records that point to non-allow-listed contigs (#85).
   This is required for processing Manta and Delly2 results, for example.
 

diff --git a/...notator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateVcf.java b/...notator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateVcf.java
@@ -829,8 +829,12 @@ private String buildGenotypeValue(VariantContext ctx, int alleleNo) {
       }
       final int[] ad = ctx.getGenotype(sample).getAD();
       int gq = ctx.getGenotype(sample).getGQ();
+      double sq = -1.0;
       if (gq == -1) {
-        gq = Integer.parseInt((String) ctx.getGenotype(sample).getExtendedAttribute("SQ", "0"));
+        sq = Double.parseDouble((String) ctx.getGenotype(sample).getExtendedAttribute("SQ", "0"));
+        if (sq == 0.0) {
+          gq = 0; // write out as int
+        }
       }
       int dp = ctx.getGenotype(sample).getDP();
       if (dp == -1) {
@@ -855,7 +859,7 @@ private String buildGenotypeValue(VariantContext ctx, int alleleNo) {
                   ",",
                   tripleQuote("gq"),
                   ":",
-                  String.valueOf(gq),
+                  (gq == -1 ? String.valueOf(sq) : String.valueOf(gq)),
                   "}"));
     }
     return "{" + Joiner.on(",").join(mappings) + "}";

diff --git a/...test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java b/...test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java
@@ -136,7 +136,7 @@ void testWithSingleton(boolean gzipOutput) throws IOException {
             + "GRCh37\t1\t1\t808928\t808928\t591\tC\tT\tsnv\t.\t.\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ad\"\"\":65,\"\"\"dp\"\"\":65,\"\"\"gq\"\"\":99}}\t1\t0\t0\t0\t0\tFALSE\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t148398\tNM_152486.2\tTRUE\t.\t.\t{\"intergenic_variant\"}\t52193\tENSG00000187634\tENST00000420190.1\tTRUE\t.\t.\t{\"intergenic_variant\"}\t51332\n"
             + "GRCh37\t1\t1\t877769\t877769\t591\tC\tT\tsnv\t.\t.\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ad\"\"\":65,\"\"\"dp\"\"\":65,\"\"\"gq\"\"\":99}}\t1\t0\t0\t0\t0\tFALSE\t1.364E-5\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t148398\tNM_152486.2\tTRUE\tc.986-21C>T\tp.=\t{\"coding_transcript_intron_variant\"}\t21\tENSG00000187634\tENST00000341065.4\tTRUE\tc.709-21C>T\tp.=\t{\"coding_transcript_intron_variant\"}\t21\n"
             + "GRCh37\t1\t1\t981952\t981952\t592\tC\tT\tsnv\t.\t.\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ad\"\"\":3,\"\"\"dp\"\"\":3,\"\"\"gq\"\"\":9}}\t1\t0\t0\t0\t0\tTRUE\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t148398\tNM_152486.2\tTRUE\t.\t.\t{\"intergenic_variant\"}\t101991\tENSG00000187634\tENST00000341065.4\tTRUE\t.\t.\t{\"intergenic_variant\"}\t101997\n"
-            + "GRCh37\t1\t1\t981953\t981953\t592\tC\tT\tsnv\t.\t.\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ad\"\"\":3,\"\"\"dp\"\"\":3,\"\"\"gq\"\"\":9}}\t1\t0\t0\t0\t0\tFALSE\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t148398\tNM_152486.2\tTRUE\t.\t.\t{\"intergenic_variant\"}\t101992\tENSG00000187634\tENST00000341065.4\tTRUE\t.\t.\t{\"intergenic_variant\"}\t101998\n";
+            + "GRCh37\t1\t1\t981953\t981953\t592\tC\tT\tsnv\t.\t.\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ad\"\"\":3,\"\"\"dp\"\"\":3,\"\"\"gq\"\"\":9.0}}\t1\t0\t0\t0\t0\tFALSE\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t148398\tNM_152486.2\tTRUE\t.\t.\t{\"intergenic_variant\"}\t101992\tENSG00000187634\tENST00000341065.4\tTRUE\t.\t.\t{\"intergenic_variant\"}\t101998\n";
     runTest(
         "bwa.gatk_hc.HG00102.vcf.gz",
         null,