Merge pull request #1124 from Clinical-Genomics/fix_vep_svsize_filter

fix: VEP filters away variants too long to annotate
Clinical-Genomics · Apr 25, 2023 · c9630fb · c9630fb
2 parents 9ba7295 + 438ce41
commit c9630fb
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/BALSAMIC/constants/workflow_params.py b/BALSAMIC/constants/workflow_params.py
@@ -153,7 +153,7 @@
         "column_info": "-c 1 -S 2 -E 3 -g 4",
     },
     "vep": {
-        "vep_filters": "--compress_output bgzip --vcf --everything --hgvsg --allow_non_variant --dont_skip --buffer_size 30000 --format vcf --offline --variant_class --merged --cache --verbose --force_overwrite"
+        "vep_filters": "--compress_output bgzip --vcf --everything --hgvsg --allow_non_variant --dont_skip --buffer_size 30000 --max_sv_size 249250621 --format vcf --offline --variant_class --merged --cache --verbose --force_overwrite"
     },
     "umicommon": {
         "align_header": "'@RG\\tID:{sample}\\tSM:{sample}\\tLB:TargetPanel\\tPL:ILLUMINA'",

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,6 +8,7 @@ Added:
 Changed:
 ^^^^^^^^
 * Fixed all conda container dependencies https://github.com/Clinical-Genomics/BALSAMIC/pull/1096
+* Changed --max_sv_size in VEP params to the size of chr1 for hg19 https://github.com/Clinical-Genomics/BALSAMIC/pull/1124
 * Increased time-limit for sambamba_exon_depth and picard_markduplicates to 6 hours https://github.com/Clinical-Genomics/BALSAMIC/pull/1143
 
 Fixed: