NCBI参考基因组下载资源

参考文件来源于GDC，提供 MD5 校验和用于在下载后验证文件完整性。

GRCh38.d1.vd1 Reference Sequence

GRCh38.d1.vd1.fa.tar.gz

• md5: 3ffbcfe2d05d43206f57f81ebb251dc9
• file size: 875.3 MB

This reference genome is used by the GDC for all sequencing and array based analyses. This file is composed of the following sequences:

• GCA_000001405.15_GRCh38_no_alt_analysis_set
• Sequence Decoys (GenBank Accession GCA_000786075)
• Virus Sequences

Index Files

Index files are built from the GDC reference genome and are used with the software listed below.

GDC.h38.d1.vd1 BWA Index Files

• GRCh38.d1.vd1_BWA.tar.gz
  • md5: 015f5223bddd93b6e8f7a038c171f7be
  • file size: 3.2 GB

GDC.h38.d1.vd1 GATK Index Files

• GRCh38.d1.vd1_GATK_indices.tar.gz
  • md5: f64be73587a7f376c0d8353f1636dca7
  • file size: 104 KB

GDC.h38.d1.vd1 STAR2 Index Files (v36)

• star-2.7.5c_GRCh38.d1.vd1_gencode.v36.tgz
  • md5: acafb76bba5e3e80eb028dc05f002ffc
  • file size: 25 GB

GDC.h38.d1.vd1 STAR2 Index Files (v22)

• star.index.genome.d1.vd1.gtfv22.tar.gz
  • md5: 7c2e6bd5767239c7c9eb618cd03bcadb
  • file size: 24.9 GB

Annotation Files

Annotation files contain information about the position and identity of regions in the reference genome. They allow software to calculate expression values.

GDC.h38 miRNA database files

• mirna_database.tar.gz
  • md5: d078aec8561d72b52e475e3f932865e4
  • file size: 185 MB

GDC.h38 GENCODE v36 GTF

• gencode.v36.annotation.gtf.gz
  • md5: c03931958d4572148650d62eb6dec41a
  • file size: 44.5 MB

GDC.h38 GENCODE v22 GTF

• gencode.v22.annotation.gtf.gz
  • md5: 291330bdcff1094bc4d5645de35e0871
  • file size: 39.0 MB

GDC.h38 GENCODE TSV (v22)

• gencode.gene.info.v22.tsv
  • md5: 0a3f1d9b0a679e2a426de36d8d74fbf9
  • file size: 6 MB

Miscellaneous Files

Methylation Array Gene Annotation File (v36)

• EPIC.hg38.manifest.gencode.v36.tsv.gz
  • md5: 071d925096dce531739cfb955605217b
  • file size: 29.9 MB
• HM27.hg38.manifest.gencode.v36.tsv.gz
  • md5: 9d4e032a9bd13127ffb9782f66450fd6
  • file size: 1.7 MB
• HM450.hg38.manifest.gencode.v36.tsv.gz
  • md5: e163fc110043abb5a7ef623816383bb9
  • file size: 17.6 MB

Antibody Description Files for TCGA RPPA Data (v36)

• TCGA_antibodies_descriptions.gencode.v36.tsv
  • md5: 1e3bed697ed431b16ba2a4dae8f52fd1
  • file size: 35 KB

Antibody Description Files for TCGA RPPA Data (v22)

• TCGA_antibodies_descriptions.gencode.v22.tsv
  • md5: b5d84afabed98a034121372df01d726f
  • file size: 35 KB

Genome Annotation Files for Legacy TCGA Data

• TCGA.hg19.June2011.gaf
  • md5: b9e0c2b81736d82d62bb6ab8cc517644
  • file size: 629 MB
• TCGA.hg18.Feb2011.gaf
  • md5: 9a5c05c5b836ec19517871f30f2bccba
  • file size: 558 MB

SNP6 GRCh38 Remapped Probeset File for Copy Number Variation Analysis

• snp6.na35.remap.hg38.subset.txt.gz
  • md5: 051457f33d264d74825a41d6b0378ac4
  • file size: 14.1 MB
  • Data Release 12 and after

If you are using Masked Copy Number Segment for GISTIC analysis, please only keep probesets with freqcnv = FALSE

SNP6 GRCh38 Liftover Probeset File for Copy Number Variation Analysis

• snp6.na35.liftoverhg38.txt.zip
  • md5: 0f982112bc81f31f1ad49a785a10305f
  • file size: 14.4 MB
  • Before Data Release 12

GDC VEP Cache File

• homo_sapiens.tar.gz
  • md5: 57064d0b081f0b99b2663977121f23c5
  • file size: 4.6 GB

GDC Panel of Normal (PON) Files used for Variant Calling

THESE FILES ARE CONTROLLED AND REQUIRE DBGAP ACCESS TO DOWNLOAD. YOU WILL NEED TO USE THE GDC-CLIENT TO DOWNLOAD THESE.

For Tumor-Only Variant Calling Pipeline

gatk4_mutect2_4136_pon.vcf.tar

• uuid: 6c4c4a48-3589-4fc0-b1fd-ce56e88c06e4
• md5: 725d891e02ca93edaabac8b09322439e
• file size: 92 MB

For Tumor / Normal Variant Calling Pipeline

MuTect2.PON.4136.vcf.tar

• uuid: 6b45b9f7-893e-4947-83b6-db0402471e23
• md5: d13a138dcf4e9f1ec8a69ac3a4f64ca9
• file size: 121 MB

MuTect2.PON.5210.vcf.tar

• uuid: 726e24c0-d2f2-41a8-9435-f85f22e1c832
• md5: 5b5c1c3e208aa9a403cc4a8ff39e7f1f
• file size: 146 MB