- How to download dbSNP153 in hg38 human genome reference
wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz.md5 wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz.tbi wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz.tbi.md5 wget https://raw.githubusercontent.com/Shicheng-Guo/AnnotationDatabase/master/GCF_000001405.38_GRCh38.p12_assembly_report.txt gawk -v RS="(\r)?\n" 'BEGIN { FS="\t" } !/^#/ { if ($10 != "na") print $7,$10; else print $7,$5 }' GCF_000001405.38_GRCh38.p12_assembly_report.txt > dbSNP-to-UCSC-GRCh38.p12.map perl -p -i -e '{s/chr//}' dbSNP-to-UCSC-GRCh38.p12.map bcftools annotate --rename-chrs dbSNP-to-UCSC-GRCh38.p12.map GCF_000001405.38.gz | gawk '/^#/ && !/^##contig=/ { print } !/^#/ { if( $1!="na" ) print }' | bgzip -c > GCF_000001405.38.dbSNP153.GRCh38p12b.GATK.vcf.gz - How to download dbSNP153 in hg19 human genome reference
wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.25.gz wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.25.gz.md5 wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.25.gz.tbi wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.25.gz.tbi.md5 - How to change GTEx eQTL
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