GET-Evidence

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