feat: add seqc2 wgs and ffpe to presets (#82)

snakemake-workflows · Jun 20, 2024 · c475b0f · c475b0f
1 parent 111b4ec
commit c475b0f
Showing 1 changed file with 19 additions and 0 deletions.
diff --git a/workflow/resources/presets.yaml b/workflow/resources/presets.yaml
@@ -20,6 +20,25 @@ benchmarks:
       - TVAF # name of tumor variant allele frequency
     high-coverage: true
 
+  seqc2-wgs:
+    genome: seqc2-somatic
+    bam-url: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/WGS/WGS_NS_T_1.bwa.dedup.bam
+    grch37: false
+    vaf-field:
+      - INFO # either FORMAT or INFO
+      - TVAF # name of tumor variant allele frequency
+    high-coverage: true
+
+  seqc2-ffpe:
+    genome: seqc2-somatic
+    bam-url: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/FFX/FFX_IL_T_24h_1.bwa.dedup.bam
+    target-regions: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/technical/reference_genome/Exome_Target_bed/S07604624_Covered_human_all_v6_plus_UTR.liftover.to.hg38.bed6.gz
+    grch37: false
+    vaf-field:
+      - INFO # either FORMAT or INFO
+      - TVAF # name of tumor variant allele frequency
+    high-coverage: true
+
   imgag-5:
     genome: na12878-somatic
     bam-url: https://download.imgag.de/public/validation_dataset_somatic/NA12878x3_23_NA12877_21_5.bam