Support #927

Update 1000 Genomes frequency data

Added by Tom Clegg over 9 years ago. Updated over 9 years ago.

Status:
In Progress
Priority:
Normal
Assigned To:
-
Target version:
-
Start date:
05/18/2012
Due date:
% Done:

0%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
Story points:
-

1kg_and_get-evidence_dbsnp_ids (31.4 KB) 1kg_and_get-evidence_dbsnp_ids Tom Clegg, 05/18/2012 03:15 PM

Associated revisions

Revision 5ca35727 (diff)
Added by Tom Clegg over 9 years ago

tweaks to make 1000 Genomes update go more smoothly. refs #927

History

#1 Updated by Tom Clegg over 9 years ago

Notes

zcat ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz | \
 egrep -v '^#' | \
 cut -f3 | \
 egrep ^rs | \
 sort > 1kg_dbsnp_ids
echo 'select variant_rsid from variants where variant_gene is null' | \
 mysql -u evidence -p evidence | \
 sed -e 's/^/rs/' | \
 sort > get-evidence_dbsnp_ids
join get-evidence_dbsnp_ids 1kg_dbsnp_ids > 1kg_and_get-evidence_dbsnp_ids

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