#938 - gnomAD download scripts

SACGF · Nov 16, 2023 · f3700c6 · f3700c6
1 parent 0d2bc83
commit f3700c6
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Showing 3 changed files with 54 additions and 4 deletions.
diff --git a/annotation/annotation_data/generate_annotation/gnomad4_download_structural.sh b/annotation/annotation_data/generate_annotation/gnomad4_download_structural.sh
@@ -3,10 +3,10 @@
 THIS_DIR=$(realpath "$(dirname "${BASH_SOURCE[0]}")")
 
 # Structural variants
-SV_COLUMNS=SVLEN,SVTYPE,END
-COLS=AC,AN,AF
-OTHER_COUNTS=N_HOMREF,N_HET,N_HOMALT
-SUBPOPS=afr_AF,amr_AF,asj_AF,eas_AF,fin_AF,mid_AF,nfe_AF,oth_AF,sas_AF
+SV_COLUMNS=INFO/SVLEN,INFO/SVTYPE,INFO/END
+COLS=INFO/AC,INFO/AN,INFO/AF
+OTHER_COUNTS=INFO/N_HOMREF,INFO/N_HET,INFO/N_HOMALT
+SUBPOPS=INFO/afr_AF,INFO/amr_AF,INFO/asj_AF,INFO/eas_AF,INFO/fin_AF,INFO/mid_AF,INFO/nfe_AF,INFO/oth_AF,INFO/sas_AF
 
 KEEP_COLUMNS=${SV_COLUMNS},${COLS},${OTHER_COUNTS},${SUBPOPS}
 CHROM_MAPPING_FILE=${THIS_DIR}/../../../snpdb/genome/chrom_mapping_GRCh38.map

diff --git a/snpdb/genome/chrom_mapping_GRCh37.map b/snpdb/genome/chrom_mapping_GRCh37.map
@@ -23,3 +23,28 @@
 X	NC_000023.10
 Y	NC_000024.9
 MT	NC_012920.1
+chr1	NC_000001.10
+chr2	NC_000002.11
+chr3	NC_000003.11
+chr4	NC_000004.11
+chr5	NC_000005.9
+chr6	NC_000006.11
+chr7	NC_000007.13
+chr8	NC_000008.10
+chr9	NC_000009.11
+chr10	NC_000010.10
+chr11	NC_000011.9
+chr12	NC_000012.11
+chr13	NC_000013.10
+chr14	NC_000014.8
+chr15	NC_000015.9
+chr16	NC_000016.9
+chr17	NC_000017.10
+chr18	NC_000018.9
+chr19	NC_000019.9
+chr20	NC_000020.10
+chr21	NC_000021.8
+chr22	NC_000022.10
+chrX	NC_000023.10
+chrY	NC_000024.9
+chrMT	NC_012920.1
diff --git a/snpdb/genome/chrom_mapping_GRCh38.map b/snpdb/genome/chrom_mapping_GRCh38.map
@@ -23,3 +23,28 @@
 X	NC_000023.11
 Y	NC_000024.10
 MT	NC_012920.1
+chr1	NC_000001.11
+chr2	NC_000002.12
+chr3	NC_000003.12
+chr4	NC_000004.12
+chr5	NC_000005.10
+chr6	NC_000006.12
+chr7	NC_000007.14
+chr8	NC_000008.11
+chr9	NC_000009.12
+chr10	NC_000010.11
+chr11	NC_000011.10
+chr12	NC_000012.12
+chr13	NC_000013.11
+chr14	NC_000014.9
+chr15	NC_000015.10
+chr16	NC_000016.10
+chr17	NC_000017.11
+chr18	NC_000018.10
+chr19	NC_000019.10
+chr20	NC_000020.11
+chr21	NC_000021.9
+chr22	NC_000022.11
+chrX	NC_000023.11
+chrY	NC_000024.10
+chrMT	NC_012920.1