feat: adding 50bp filter for REF/ALT on clinvar-sv import (#293) (#294)

varfish-org · Nov 16, 2023 · 831830a · 831830a
1 parent 1837899
commit 831830a
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Showing 8 changed files with 30 additions and 29 deletions.
diff --git a/src/clinvar_sv/cli/import.rs b/src/clinvar_sv/cli/import.rs
@@ -21,6 +21,9 @@ pub struct Args {
     #[arg(long)]
     pub path_out_rocksdb: String,
 
+    /// Minimal VCF REF/ALT length to consider as SV.
+    #[arg(long, default_value_t = 50)]
+    pub min_var_size: u32,
     /// Name of the column family to import into.
     #[arg(long, default_value = "clinvar-sv")]
     pub cf_name: String,
@@ -89,6 +92,23 @@ fn jsonl_import(
             outer_stop,
         } = sequence_location;
 
+        if let (Some(reference_allele_vcf), Some(alternate_allee_vcf)) =
+            (reference_allele_vcf.as_ref(), alternate_allele_vcf.as_ref())
+        {
+            if reference_allele_vcf.len() < args.min_var_size as usize
+                && alternate_allee_vcf.len() < args.min_var_size as usize
+            {
+                tracing::debug!(
+                    "skipping line because of short REF/ALT: {}/{}: {}>{}",
+                    &vcv,
+                    &rcv,
+                    reference_allele_vcf,
+                    alternate_allee_vcf,
+                );
+                continue;
+            }
+        }
+
         let (start, stop, inner_start, inner_stop, outer_start, outer_stop) =
             if let (Some(start), Some(stop)) = (start, stop) {
                 (
@@ -267,6 +287,7 @@ mod test {
                 String::from("tests/clinvar-sv/clinvar-variants-grch37-strucvars.jsonl"),
             ],
             path_out_rocksdb: format!("{}", tmp_dir.join("out-rocksdb").display()),
+            min_var_size: 50,
             cf_name: String::from("clinvar-sv"),
             cf_name_by_rcv: String::from("clinvar-sv-by-rcv"),
             path_wal_dir: None,

diff --git a/...clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap b/...clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap
@@ -2,26 +2,6 @@
 source: src/clinvar_sv/cli/query.rs
 expression: "&out_data"
 ---
-{"release":"GRCh37","chromosome":"22","start":41320486,"stop":41320486,"reference":"G","alternative":"T","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000051","reference_assertions":[{"rcv":"RCV000000068","title":"NM_022098.4(XPNPEP3):c.1357G>T (p.Gly453Cys) AND Nephronophthisis-like nephropathy 1","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"22","start":41305199,"stop":41305202,"reference":"TCAAA","alternative":"T","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":0,"vcv":"VCV000000052","reference_assertions":[{"rcv":"RCV000000069","title":"NM_022098.4(XPNPEP3):c.931_934del (p.Asn311fs) AND Nephronophthisis-like nephropathy 1","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"15","start":49048486,"stop":49048486,"reference":"G","alternative":"A","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000056","reference_assertions":[{"rcv":"RCV000000073","title":"NM_001194998.2(CEP152):c.2959C>T (p.Arg987Ter) AND Microcephaly 9, primary, autosomal recessive","clinical_significance":1,"review_status":3}]}
-{"release":"GRCh37","chromosome":"19","start":45315576,"stop":45315576,"reference":"C","alternative":"T","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000443","reference_assertions":[{"rcv":"RCV000000472","title":"NM_005581.5(BCAM):c.361C>T (p.Arg121Ter) AND BLOOD GROUP--LUTHERAN NULL","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98304466,"stop":98304466,"reference":"G","alternative":"A","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000451","reference_assertions":[{"rcv":"RCV000000480","title":"NM_000097.7(CPOX):c.991C>T (p.Arg331Trp) AND Coproporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98311840,"stop":98311860,"reference":"TACCTGTGCCAGAGCCTGGCAC","alternative":"T","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":0,"vcv":"VCV000000455","reference_assertions":[{"rcv":"RCV000000484","title":"NM_000097.7(CPOX):c.489_509del (p.Cys164_Val170del) AND Coproporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98307627,"stop":98307627,"reference":"G","alternative":"C","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000456","reference_assertions":[{"rcv":"RCV000000485","title":"NM_000097.7(CPOX):c.883C>G (p.His295Asp) AND Coproporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98300248,"stop":98300248,"reference":"T","alternative":"C","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000457","reference_assertions":[{"rcv":"RCV000000486","title":"NM_000097.7(CPOX):c.1277+3A>G AND Harderoporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98309933,"stop":98309933,"reference":"G","alternative":"A","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000460","reference_assertions":[{"rcv":"RCV000000489","title":"NM_000097.7(CPOX):c.623C>T (p.Ser208Phe) AND Coproporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98304475,"stop":98304475,"reference":"G","alternative":"A","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000461","reference_assertions":[{"rcv":"RCV000000490","title":"NM_000097.7(CPOX):c.982C>T (p.Arg328Cys) AND Coproporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98307653,"stop":98307654,"reference":"G","alternative":"GT","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":1,"vcv":"VCV000000462","reference_assertions":[{"rcv":"RCV000000491","title":"NM_000097.7(CPOX):c.856dup (p.Thr286fs) AND Coproporphyria","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"3","start":98307675,"stop":98307675,"reference":"C","alternative":"G","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000463","reference_assertions":[{"rcv":"RCV000000492","title":"NM_000097.7(CPOX):c.835G>C (p.Gly279Arg) AND Coproporphyria, digenic","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"11","start":112104201,"stop":112104214,"reference":"AGTTCTTCCTGTAGG","alternative":"A","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":0,"vcv":"VCV000000478","reference_assertions":[{"rcv":"RCV000000507","title":"NM_000317.3(PTS):c.361_374del (p.Val121fs) AND Hyperphenylalaninemia, bh4-deficient, a, due to partial pts deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"11","start":112099372,"stop":112099372,"reference":"A","alternative":"G","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000482","reference_assertions":[{"rcv":"RCV000000511","title":"NM_000317.3(PTS):c.139A>G (p.Asn47Asp) AND Hyperphenylalaninemia, bh4-deficient, a, due to partial pts deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"4","start":17503409,"stop":17503410,"reference":"G","alternative":"GGTA","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":1,"vcv":"VCV000000489","reference_assertions":[{"rcv":"RCV000000518","title":"NM_000320.3(QDPR):c.366_368dup (p.Thr123dup) AND Dihydropteridine reductase deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"4","start":17503456,"stop":17503456,"reference":"A","alternative":"C","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000491","reference_assertions":[{"rcv":"RCV000000520","title":"NM_000320.3(QDPR):c.322T>G (p.Trp108Gly) AND Dihydropteridine reductase deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"4","start":17510986,"stop":17510986,"reference":"A","alternative":"G","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000492","reference_assertions":[{"rcv":"RCV000000521","title":"NM_000320.3(QDPR):c.106T>C (p.Trp36Arg) AND Dihydropteridine reductase deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"4","start":17493951,"stop":17493951,"reference":"T","alternative":"C","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000494","reference_assertions":[{"rcv":"RCV000000523","title":"NM_000320.3(QDPR):c.449A>G (p.Tyr150Cys) AND Dihydropteridine reductase deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"4","start":17506027,"stop":17506027,"reference":"C","alternative":"T","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000495","reference_assertions":[{"rcv":"RCV000000524","title":"NM_000320.3(QDPR):c.270G>A (p.Trp90Ter) AND Dihydropteridine reductase deficiency","clinical_significance":0,"review_status":5}]}
-{"release":"GRCh37","chromosome":"6","start":117198947,"stop":117198947,"reference":"A","alternative":"G","inner_start":null,"inner_stop":null,"outer_start":null,"outer_stop":null,"variant_type":5,"vcv":"VCV000000497","reference_assertions":[{"rcv":"RCV000000526","title":"NM_173560.4(RFX6):c.224-12A>G AND Hypoplastic pancreas-intestinal atresia-hypoplastic gallbalder syndrome","clinical_significance":0,"review_status":5}]}
 {"release":"GRCh37","chromosome":"X","start":155210040,"stop":155242832,"reference":null,"alternative":null,"inner_start":155210040,"inner_stop":null,"outer_start":155242832,"outer_stop":null,"variant_type":0,"vcv":"VCV000057500","reference_assertions":[{"rcv":"RCV000051210","title":"GRCh38/hg38 Xq28(chrX:155980375-156013167)x0 AND See cases","clinical_significance":4,"review_status":3}]}
 {"release":"GRCh37","chromosome":"7","start":64691936,"stop":64866073,"reference":null,"alternative":null,"inner_start":64691936,"inner_stop":null,"outer_start":64866073,"outer_stop":null,"variant_type":0,"vcv":"VCV000057566","reference_assertions":[{"rcv":"RCV000051294","title":"GRCh38/hg38 7q11.21(chr7:65231558-65401160)x1 AND See cases","clinical_significance":2,"review_status":3}]}
 {"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"reference":null,"alternative":null,"inner_start":34150132,"inner_stop":null,"outer_start":34182300,"outer_stop":null,"variant_type":0,"vcv":"VCV000057627","reference_assertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","clinical_significance":0,"review_status":3}]}

diff --git a/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/000016.sst b/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/000016.sst
diff --git a/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/000018.sst b/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/000018.sst
diff --git a/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/000020.sst b/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/000020.sst
diff --git a/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/IDENTITY b/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/IDENTITY
diff --git a/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/LOG b/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/LOG
diff --git a/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/MANIFEST-000005 b/tests/clinvar-sv/clinvar-sv-grch37.tsv.db/MANIFEST-000005