Merge pull request #34 from ghga-de/33-filter-mq-is-not-defined-in-th…

…e-header

MQ added into FILTER

.gitignore

@@ -15,4 +15,5 @@ test_output/
 tests/data/
 work/
 .github/CODEOWNERS-tmp
-bin/vcfparser.pyc
+bin/vcfparser.pyc
+node_modules/*

.gitpod.yml

@@ -0,0 +1,10 @@
+# This configuration file was automatically generated by Gitpod.
+# Please adjust to your needs (see https://www.gitpod.io/docs/introduction/learn-gitpod/gitpod-yaml)
+# and commit this file to your remote git repository to share the goodness with others.
+
+# Learn more from ready-to-use templates: https://www.gitpod.io/docs/introduction/getting-started/quickstart
+
+tasks:
+  - init: npm install
+
+

assets/config/convertToStdVCF.json

@@ -64,10 +64,10 @@
       "type": "Flag",
       "description": "Strand bias of reads with mutant allele = zero reads on one strand and variant allele frequency below 0.1"
     },
-    "FRQ": {
+    "FREQ": {
       "number": "0",
       "type": "Flag",
-      "description": "variant allele frequency below 0.05"
+      "description": "Variant allele frequency above 0.001 in GnomAD or above 0.001 in local control database"
     },
     "TAR": {
       "number": "0",
@@ -97,7 +97,7 @@
     "ALTC": {
       "number": "0",
       "type": "Flag",
-      "description": "Alternative reads in control"
+      "description": "Alternative reads in control and other filter not PASS"
     },
     "ALTCFR": {
       "number": "0",
@@ -117,7 +117,7 @@
     "VAF": {
       "number": "0",
       "type": "Flag",
-      "description": "Variant allele frequency in tumor < ' + str(args.newpun) + ' times allele frequency in control"
+      "description": "Variant allele frequency in tumor < 10% and other filter not PASS"
     },
     "TSR_ctrl": {
       "number": "0",
@@ -167,7 +167,7 @@
     "QD": {
       "number": "1",
       "type": "Float",
-      "description": "Variant-quality/read-depth for this variant"
+      "description": "Variants fail quality/depth filter."
     },
     "Q20": {
       "number": "0",
@@ -198,6 +198,16 @@
       "number": "0",
       "type": "Flag",
       "description": "Too many haplotypes are supported by the data in this region."
+    },
+    "MQ": {
+      "number": "0",
+      "type": "Flag",
+      "description": "Root-mean-square mapping quality across calling region is low"
+    },
+    "SC": {
+      "number": "0",
+      "type": "Flag",
+      "description": "Variants fail sequence-context filter. Surrounding sequence is low-complexity"
     }
   },