fix test

KalinNonchev · Nov 4, 2023 · 6bb0a4c · 6bb0a4c
1 parent 34240b2
commit 6bb0a4c
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/gnomad_db/pkgdata/gnomad_columns.yaml b/gnomad_db/pkgdata/gnomad_columns.yaml
@@ -27,17 +27,16 @@ v3:
     - AC # Alternate allele count for samples
     - AN # Total number of alleles in samples
     - AF # Alternate allele frequency in samples
-    - rf_tp_probability # Random forest prediction probability for a site being a true variant
+    - InbreedingCoeff # Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation
     - MQ # Root mean square of the mapping quality of reads across all samples
     - QD # Variant call confidence normalized by depth of sample reads supporting a variant
     - ReadPosRankSum # Z-score from Wilcoxon rank sum test of alternate vs. reference read position bias
-    - DP # Depth of informative coverage for each sample; reads with MQ=255 or with bad mates are filtered
-    - VQSLOD # Log-odds ratio of being a true variant versus being a false positive under the trained VQSR Gaussian mixture model
+    - VarDP
+    - AS_VQSLOD
     - AC_popmax # Allele count in the population with the maximum AF
     - AN_popmax # Total number of alleles in the population with the maximum AF
     - AF_popmax # Maximum allele frequency across populations (excluding samples of Ashkenazi
     - AF_eas # Alternate allele frequency in samples of East Asian ancestry
-    - AF_oth # Alternate allele frequency in XY samples of Other ancestry
     - AF_nfe # Alternate allele frequency in XY samples of Non-Finnish European ancestry
     - AF_fin # Alternate allele frequency in XX samples of Finnish ancestry
     - AF_afr # Alternate allele frequency in samples of African/African-American ancestry

diff --git a/script_config.yaml b/script_config.yaml
@@ -2,5 +2,5 @@ database_location: "test_out" # where to create the database, make sure you have
 gnomad_vcf_location: "data" # where are your *.vcf.bgz located
 tables_location: "test_out" # where to store the preprocessed intermediate files, you can leave it like this 
 script_locations: "test_out" # where to store the scripts, where you can check the progress of your jobs, you can leave it like this
-gnomad_version: "v3" # main gnomad_version version of the gnomAD vcf file (e.g., v2, v3, v4)
+gnomad_version: "v2" # main gnomad_version version of the gnomAD vcf file (e.g., v2, v3, v4)
 KERNEL: "gnomad_db"