Adding Read depth from ExAC and GNOMAD

macarthur-lab · Aug 29, 2017 · 1bdcf56 · 1bdcf56
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diff --git a/output/b37/multi/clinvar_allele_trait_pairs.multi.b37.tsv.gz b/output/b37/multi/clinvar_allele_trait_pairs.multi.b37.tsv.gz
diff --git a/output/b37/multi/clinvar_allele_trait_pairs.multi.b37.tsv.gz.tbi b/output/b37/multi/clinvar_allele_trait_pairs.multi.b37.tsv.gz.tbi
diff --git a/output/b37/multi/clinvar_allele_trait_pairs_example_750_rows.multi.b37.tsv b/output/b37/multi/clinvar_allele_trait_pairs_example_750_rows.multi.b37.tsv
diff --git a/output/b37/multi/clinvar_alleles.multi.b37.tsv.gz b/output/b37/multi/clinvar_alleles.multi.b37.tsv.gz
diff --git a/output/b37/multi/clinvar_alleles.multi.b37.tsv.gz.tbi b/output/b37/multi/clinvar_alleles.multi.b37.tsv.gz.tbi
diff --git a/output/b37/multi/clinvar_alleles.multi.b37.vcf.gz b/output/b37/multi/clinvar_alleles.multi.b37.vcf.gz
diff --git a/output/b37/multi/clinvar_alleles.multi.b37.vcf.gz.tbi b/output/b37/multi/clinvar_alleles.multi.b37.vcf.gz.tbi
diff --git a/output/b37/multi/clinvar_alleles_example_750_rows.multi.b37.tsv b/output/b37/multi/clinvar_alleles_example_750_rows.multi.b37.tsv
diff --git a/output/b37/multi/clinvar_alleles_example_750_rows.multi.b37.vcf b/output/b37/multi/clinvar_alleles_example_750_rows.multi.b37.vcf
diff --git a/output/b37/multi/clinvar_alleles_stats.multi.b37.txt b/output/b37/multi/clinvar_alleles_stats.multi.b37.txt
@@ -10,13 +10,13 @@ Distinct chromosomes      2
 Name: variation_type, dtype: int64
 ================
 column 17: clinical_significance
--                                                            263
-Pathogenic                                                    71
-Conflicting interpretations of pathogenicity                  31
+-                                                            262
+Pathogenic                                                    72
+Conflicting interpretations of pathogenicity                  33
 Uncertain significance                                        17
 Benign                                                        16
 other                                                         15
-Benign/Likely benign                                          14
+Benign/Likely benign                                          12
 not provided                                                   9
 Pathogenic/Likely pathogenic                                   9
 Likely pathogenic                                              6
@@ -35,20 +35,20 @@ Pathogenic, risk factor                                        1
 Name: clinical_significance, dtype: int64
 ================
 column 24: review_status
-no assertion for the individual variant                 371
-no assertion criteria provided                           38
-criteria provided, multiple submitters, no conflicts     28
-criteria provided, single submitter                      22
-criteria provided, conflicting interpretations           18
-no assertion provided                                     2
+no assertion for the individual variant                 368
+no assertion criteria provided                           36
+criteria provided, multiple submitters, no conflicts     31
+criteria provided, conflicting interpretations           20
+criteria provided, single submitter                      18
+no assertion provided                                     6
 practice guideline                                        1
 reviewed by expert panel                                  1
 Name: review_status, dtype: int64
 ================
 column 38: gold_stars
-0    411
-1     40
-2     28
+0    410
+1     38
+2     31
 4      1
 3      1
 Name: gold_stars, dtype: int64

diff --git a/output/b37/multi/clinvar_alleles_with_exac_v1.multi.b37.tsv.gz b/output/b37/multi/clinvar_alleles_with_exac_v1.multi.b37.tsv.gz
diff --git a/output/b37/multi/clinvar_alleles_with_exac_v1.multi.b37.tsv.gz.tbi b/output/b37/multi/clinvar_alleles_with_exac_v1.multi.b37.tsv.gz.tbi
diff --git a/output/b37/multi/clinvar_alleles_with_exac_v1_example_750_rows.multi.b37.tsv b/output/b37/multi/clinvar_alleles_with_exac_v1_example_750_rows.multi.b37.tsv
diff --git a/output/b37/multi/clinvar_alleles_with_gnomad_exomes.multi.b37.tsv.gz b/output/b37/multi/clinvar_alleles_with_gnomad_exomes.multi.b37.tsv.gz
diff --git a/output/b37/multi/clinvar_alleles_with_gnomad_exomes.multi.b37.tsv.gz.tbi b/output/b37/multi/clinvar_alleles_with_gnomad_exomes.multi.b37.tsv.gz.tbi
diff --git a/output/b37/multi/clinvar_alleles_with_gnomad_exomes_example_750_rows.multi.b37.tsv b/output/b37/multi/clinvar_alleles_with_gnomad_exomes_example_750_rows.multi.b37.tsv
diff --git a/output/b37/multi/clinvar_alleles_with_gnomad_genomes.multi.b37.tsv.gz b/output/b37/multi/clinvar_alleles_with_gnomad_genomes.multi.b37.tsv.gz
diff --git a/output/b37/multi/clinvar_alleles_with_gnomad_genomes.multi.b37.tsv.gz.tbi b/output/b37/multi/clinvar_alleles_with_gnomad_genomes.multi.b37.tsv.gz.tbi
diff --git a/output/b37/multi/clinvar_alleles_with_gnomad_genomes_example_750_rows.multi.b37.tsv b/output/b37/multi/clinvar_alleles_with_gnomad_genomes_example_750_rows.multi.b37.tsv
diff --git a/output/b37/single/clinvar_allele_trait_pairs.single.b37.tsv.gz b/output/b37/single/clinvar_allele_trait_pairs.single.b37.tsv.gz
diff --git a/output/b37/single/clinvar_allele_trait_pairs.single.b37.tsv.gz.tbi b/output/b37/single/clinvar_allele_trait_pairs.single.b37.tsv.gz.tbi
diff --git a/output/b37/single/clinvar_allele_trait_pairs_example_750_rows.single.b37.tsv b/output/b37/single/clinvar_allele_trait_pairs_example_750_rows.single.b37.tsv
diff --git a/output/b37/single/clinvar_alleles.single.b37.tsv.gz b/output/b37/single/clinvar_alleles.single.b37.tsv.gz
diff --git a/output/b37/single/clinvar_alleles.single.b37.tsv.gz.tbi b/output/b37/single/clinvar_alleles.single.b37.tsv.gz.tbi
diff --git a/output/b37/single/clinvar_alleles.single.b37.vcf.gz b/output/b37/single/clinvar_alleles.single.b37.vcf.gz
diff --git a/output/b37/single/clinvar_alleles.single.b37.vcf.gz.tbi b/output/b37/single/clinvar_alleles.single.b37.vcf.gz.tbi
diff --git a/output/b37/single/clinvar_alleles_example_750_rows.single.b37.tsv b/output/b37/single/clinvar_alleles_example_750_rows.single.b37.tsv
diff --git a/output/b37/single/clinvar_alleles_example_750_rows.single.b37.vcf b/output/b37/single/clinvar_alleles_example_750_rows.single.b37.vcf