fixing gnomad_popmax annotation

Clinical-Genomics · Sep 21, 2021 · 514ec3a · 514ec3a
1 parent 5160f29
commit 514ec3a
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Showing 12 changed files with 16 additions and 16 deletions.
diff --git a/definitions/dragen_rd_dna_parameters.yaml b/definitions/dragen_rd_dna_parameters.yaml
@@ -200,7 +200,7 @@ sv_fqa_vcfanno_filters:
   data_type: ARRAY
   default:
     - GNOMADAF
-    - GNOMADAF_POPMAX
+    - GNOMADAF_popmax
   type: recipe_argument
 sv_bcftools_view_filter:
   associated_recipe:

diff --git a/definitions/rd_dna_vcf_rerun_parameters.yaml b/definitions/rd_dna_vcf_rerun_parameters.yaml
@@ -168,7 +168,7 @@ sv_fqa_vcfanno_filters:
   data_type: ARRAY
   default:
     - GNOMADAF
-    - GNOMADAF_POPMAX
+    - GNOMADAF_popmax
   type: recipe_argument
 sv_bcftools_view_filter:
   associated_recipe:

diff --git a/lib/MIP/Program/Bcftools.pm b/lib/MIP/Program/Bcftools.pm
@@ -1097,7 +1097,7 @@ sub bcftools_mpileup {
         stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
         stdoutfile_path        => { store => \$stdoutfile_path,        strict_type => 1, },
         targets                => {
-            store       => $targets,
+            store       => \$targets,
             strict_type => 1,
         },
         threads => {

diff --git a/t/data/references/grch37_frequency_vcfanno_filter_config_-v1.0-.toml b/t/data/references/grch37_frequency_vcfanno_filter_config_-v1.0-.toml
@@ -1,19 +1,19 @@
 # TOML
 
-title = "Vcfanno configuration file" 
+title = "Vcfanno configuration file"
 
 [[annotation]]
 file="/mnt/hds/proj/cust003/develop/mip_references/grch37_gnomad.genomes_-r2.0.1-.vcf.gz"
 fields = ["AF", "AF_POPMAX"]
 ops=["self", "self"]
-names=["GNOMADAF", "GNOMADAF_POPMAX"]
+names=["GNOMADAF", "GNOMADAF_popmax"]
 skip_split_and_normalize = true
 
 [[annotation]]
 file="/mnt/hds/proj/cust003/develop/mip_references/grch37_gnomad.genomes_-r2.1.1-.vcf.gz"
 fields = ["AF", "AF_POPMAX"]
 ops=["self", "self"]
-names=["GNOMADAF", "GNOMADAF_POPMAX"]
+names=["GNOMADAF", "GNOMADAF_popmax"]
 
 [[annotation]]
 file="/mnt/hds/proj/cust003/develop/mip_references/grch37_cadd_whole_genome_snvs_-v1.4-.tsv.gz"

diff --git a/t/data/references/grch37_frequency_vcfanno_filter_config_bad_data_-v1.0-.toml b/t/data/references/grch37_frequency_vcfanno_filter_config_bad_data_-v1.0-.toml
@@ -1,9 +1,9 @@
 # TOML
 
-title = "Vcfanno configuration file" 
+title = "Vcfanno configuration file"
 
 [[annotation]]
 file="/mnt/hds/proj/cust003/develop/mip_references/grch37_gnomad.genomes_-r2.0.1-.vcf.gz"
 #fields = ["AF", "AF_POPMAX"]
 ops=["self", "self"]
-names=["GNOMADAF", "GNOMADAF_POPMAX"]
+names=["GNOMADAF", "GNOMADAF_popmax"]
diff --git a/t/data/references/grch37_vcfanno_config_bad_template-v1.0-.toml b/t/data/references/grch37_vcfanno_config_bad_template-v1.0-.toml
@@ -1,6 +1,6 @@
 # TOML
 
-title = "Vcfanno configuration file" 
+title = "Vcfanno configuration file"
 
 [functions]
 file = "TEST_REFERENCES!/vcfanno_functions_-v1.0-.lua"
@@ -9,4 +9,4 @@ file = "TEST_REFERENCES!/vcfanno_functions_-v1.0-.lua"
 file="TEST_REFERENCES!/grch37_gnomad.genomes_-r2.0.1-.vcf.gz"
 fields = ["AF", "AF_POPMAX", "MISSING_TAG"]
 ops=["self", "self", "self"]
-names=["GNOMADAF", "GNOMADAF_POPMAX", "MISSING_TAG"]
+names=["GNOMADAF", "GNOMADAF_popmax", "MISSING_TAG"]
diff --git a/t/data/references/grch37_vcfanno_config_template-v1.0-.toml b/t/data/references/grch37_vcfanno_config_template-v1.0-.toml
@@ -15,5 +15,5 @@ names=["Obs", "Hom"]
 file="TEST_REFERENCES!/grch37_gnomad.genomes_-r2.0.1-.vcf.gz"
 fields = ["AF", "AF_POPMAX"]
 ops=["self", "self"]
-names=["GNOMADAF", "GNOMADAF_POPMAX"]
+names=["GNOMADAF", "GNOMADAF_popmax"]
 
diff --git a/t/data/references/grch38_vcfanno_config_template-v1.0-.toml b/t/data/references/grch38_vcfanno_config_template-v1.0-.toml
@@ -15,4 +15,4 @@ ops=["self", "self"]
 file="TEST_REFERENCES!/grch38_gnomad_reformated_-r3.1.1-.vcf.gz"
 fields = ["AF", "AF_popmax"]
 ops=["self", "self"]
-names=["GNOMADAF", "GNOMADAF_POPMAX"]
+names=["GNOMADAF", "GNOMADAF_popmax"]
diff --git a/t/data/test_data/test.vcf b/t/data/test_data/test.vcf
@@ -13,4 +13,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|REFSEQ_MATCH|SOURCE|GIVEN_REF|USED_REF|BAM_EDIT|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|ExACpLI|LoFtool|MES-NCSS_downstream_acceptor|MES-NCSS_downstream_donor|MES-NCSS_upstream_acceptor|MES-NCSS_upstream_donor|MES-SWA_acceptor_alt|MES-SWA_acceptor_diff|MES-SWA_acceptor_ref|MES-SWA_acceptor_ref_comp|MES-SWA_donor_alt|MES-SWA_donor_diff|MES-SWA_donor_ref|MES-SWA_donor_ref_comp|MaxEntScan_alt|MaxEntScan_diff|MaxEntScan_ref|genomic_superdups_frac_match">
 ##Software=<ID=vcfparser.pl,Version=1.2.16,Date=2019-08-05
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ACC5339A2	ACC5339A3	ACC5339A4
-1	12719	.	G	C	292.10	PASS	AC=2;AF=0.333;AN=6;ANN=C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript|2/3|n.466G>C||||||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene|2/3|n.463G>C||||||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene|2/4|n.479G>C||||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene||n.*1685C>G|||||1685|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene||n.*1692C>G|||||1692|,C|intron_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene|3/5|n.182+22G>C||||||;Annotation=DDX11L1,WASH7P;BaseQRankSum=0;CADD=3.695;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034|YES|||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|intron_variant&non_coding_transcript_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene||3/5|ENST00000450305.2:n.182+22G>C|||||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||7.609|1.139|11.897|7.154|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|2/3||ENST00000456328.2:n.466G>C||466|||||||1||HGNC|37102|YES|||||||||Ensembl|G|G||||||||||||3.895|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||1685|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|2/3||ENST00000515242.2:n.463G>C||463|||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||-0.591|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|2/4||ENST00000518655.2:n.479G>C||479|||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||11.709|7.656|4.227|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||1692|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|653635|Transcript|NR_024540.1|pseudogene|||||||||||1643|-1||EntrezGene|38034|YES|||||||||RefSeq|G|G|OK|||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|100287102|Transcript|NR_046018.2|pseudogene|2/3||NR_046018.2:n.461G>C||461|||||||1||EntrezGene|37102|YES|||||||||RefSeq|G|G||||||||||||3.895|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|MIR6859-1|102466751|Transcript|NR_106918.1|miRNA|||||||||||4650|-1||EntrezGene||YES|||||||||RefSeq|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232;DP=138;ExcessHet=4.7712;FS=0;GNOMADAF=0.0494;GNOMADAF_POPMAX=0.1274;MLEAC=2;MLEAF=0.333;MQ=25.62;MQRankSum=-0.086;NEGATIVE_TRAIN_SITE;Obs=230;QD=3.7;RankResult=-12|0|0|-12|5|0|3|0|0|3;RankScore=livingox:-13;ReadPosRankSum=0.819;SOR=0.09;SWEGENAC_Hemi=0;SWEGENAC_Het=154;SWEGENAC_Hom=0;SWEGENAF=0.077;VQSLOD=-3.219;culprit=QD;most_severe_consequence=38034:C|downstream_gene_variant,37102:C|splice_region_variant	GT:AD:DP:GQ:PL	0/1:33,7:40:89:89,0,891	0/1:28,11:39:99:214,0,726	0/0:59,0:59:53:0,53,2332
+1	12719	.	G	C	292.10	PASS	AC=2;AF=0.333;AN=6;ANN=C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript|2/3|n.466G>C||||||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene|2/3|n.463G>C||||||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene|2/4|n.479G>C||||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene||n.*1685C>G|||||1685|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene||n.*1692C>G|||||1692|,C|intron_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene|3/5|n.182+22G>C||||||;Annotation=DDX11L1,WASH7P;BaseQRankSum=0;CADD=3.695;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034|YES|||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|intron_variant&non_coding_transcript_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene||3/5|ENST00000450305.2:n.182+22G>C|||||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||7.609|1.139|11.897|7.154|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|2/3||ENST00000456328.2:n.466G>C||466|||||||1||HGNC|37102|YES|||||||||Ensembl|G|G||||||||||||3.895|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||1685|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|2/3||ENST00000515242.2:n.463G>C||463|||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||-0.591|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|2/4||ENST00000518655.2:n.479G>C||479|||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||11.709|7.656|4.227|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||1692|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|653635|Transcript|NR_024540.1|pseudogene|||||||||||1643|-1||EntrezGene|38034|YES|||||||||RefSeq|G|G|OK|||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|100287102|Transcript|NR_046018.2|pseudogene|2/3||NR_046018.2:n.461G>C||461|||||||1||EntrezGene|37102|YES|||||||||RefSeq|G|G||||||||||||3.895|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|MIR6859-1|102466751|Transcript|NR_106918.1|miRNA|||||||||||4650|-1||EntrezGene||YES|||||||||RefSeq|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232;DP=138;ExcessHet=4.7712;FS=0;GNOMADAF=0.0494;GNOMADAF_popmax=0.1274;MLEAC=2;MLEAF=0.333;MQ=25.62;MQRankSum=-0.086;NEGATIVE_TRAIN_SITE;Obs=230;QD=3.7;RankResult=-12|0|0|-12|5|0|3|0|0|3;RankScore=livingox:-13;ReadPosRankSum=0.819;SOR=0.09;SWEGENAC_Hemi=0;SWEGENAC_Het=154;SWEGENAC_Hom=0;SWEGENAF=0.077;VQSLOD=-3.219;culprit=QD;most_severe_consequence=38034:C|downstream_gene_variant,37102:C|splice_region_variant	GT:AD:DP:GQ:PL	0/1:33,7:40:89:89,0,891	0/1:28,11:39:99:214,0,726	0/0:59,0:59:53:0,53,2332
diff --git a/templates/grch38_mip_rd_dna_config.yaml b/templates/grch38_mip_rd_dna_config.yaml
@@ -68,7 +68,7 @@ vcfanno_config: grch38_vcfanno_config_-v0.2-.toml
 ## Parameters
 sv_fqa_vcfanno_filters:
   - GNOMADAF
-  - GNOMADAF_POPMAX
+  - GNOMADAF_popmax
   - SWEGENAF
   - swegen
 gatk_path: /opt/conda/opt/gatk-3.8

diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml
@@ -49,7 +49,7 @@ fqf_annotations:
   - SWEGENAF
 sv_fqa_vcfanno_filters:
   - GNOMADAF
-  - GNOMADAF_POPMAX
+  - GNOMADAF_popmax
   - gnomad_svAF
   - clinical_genomics_loqusFrq
 gatk_path: /usr

diff --git a/templates/mip_rd_dna_vcf_rerun_config.yaml b/templates/mip_rd_dna_vcf_rerun_config.yaml
@@ -46,7 +46,7 @@ fqf_annotations:
   - SWEGENAF
 sv_fqa_vcfanno_filters:
   - GNOMADAF
-  - GNOMADAF_POPMAX
+  - GNOMADAF_popmax
   - SWEGENAF
   - swegen
 picardtools_path: /usr/picard