08 January 1944
  • 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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  • All the blogs are my own and not the views of my employer
  • All the opinions are my own and not the views of my employer
  • All the contents are my own and should never be taken seriously
  • All the contents are only used for help. reminding me if misleading happens
  • All the figures are only used for non-profit education. reminding me if infrigement happens

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