CMDB:大规模中国人群体变异频率数据库
简介
CMDB(全称是Chinese Millionome Database),大约包含了9M个高质量的变异位点(约占人类基因组总长的0.003)。
数据库网站的第一版是参考ExAC做的,使用的底层框架是常见的Nginx+Flask+MongoDB。可通过Genome API访问,不过CMDB中的数据不能够被下载。
CMBD官网地址:
开发者知乎介绍:https://zhuanlan.zhihu.com/p/52238870
作者解读CMDB:https://mp.weixin.qq.com/s?__biz=MzAxOTUxOTM0Nw==&mid=2649798742&idx=1&sn=3b27cafe9ecd8ecd3c35bc1b1dbad947&chksm=83c1da4ab4b6535cd6265f600375f524ec071b8155462e5e042bfa013a42b98300b74efa740b&scene=21#wechat_redirect
Git 软件说明:https://github.com/ShujiaHuang/cmdbtools
安装
1、命令行直接安装
pip install cmdbtools
2、git安装
地址:https://github.com/ShujiaHuang/cmdbtools
pip install git+git://github.com/ShujiaHuang/cmdbtools.git#egg=cmdbtools
3、查看帮助信息
cmdbtools --help
usage: cmdbtools [-h]
{login,logout,print-access-token,annotate,query-variant} ...
Manage authentication for CMDB API and do querying from command line.
optional arguments:
-h, --help show this help message and exit
Commands:
{login,logout,print-access-token,annotate,query-variant}
login Authorize access to CMDB API.
logout Logout CMDB.
print-access-token Display access token for CMDB API.
annotate Annotate input VCF.
query-variant Query variant by variant identifier or by chromosome
name and chromosomal position.
使用
1、API使用许可
申请API AK, 提交申请:
官方批准后获得:
1.2 使用
1.2.1 登录
your-genomics-api-key为获批的API AK
cmdbtools login -k your-genomics-api-key
1.2.2 查询
1.2.2.1 位点信息查询
以 chr17-41223094-T-C 为例:
cmdbtools query-variant -c chr17 -p 41223094 > ch17_41223094.vcf
或者 以输入文件(positions.list )的形式导入要查询的位点信息
cmdbtools query-variant -l positions.list > result.vcf
positions.list如下:
#CHROM POS
chr22 17662378
chr22 17662408
22 17662442
22 17662444
22 17662699
22 17662729
22 17662766
22 17662767
22 17662793
22 17662794
22 17662853
22 17662883
chr22 17662917
22 17663530
22 17663561
22 17663586
22 17669232
22 17669238
22 17669239
22 17669241
22 17669245
22 17669265
22 17669339
22 17670869
22 17670877
22 17672663
22 17684454
22 17684466
22 17684477
22 17684546
22 17684627
22 17684643
22 17687954
22 17687992
22 17687997
22 17688069
22 17688144
22 17688167
22 17688177
22 17690290
22 17690374
22 17690382
22 17690409
22 17690423
22 17690424
22 17690425
22 17690428
22 17690428
22 17690429
22 17690429
22 17690468
22 17690485
22 17690496
22 17662353 17663671
22 17669209 17669357
1.2.2.2 注释到vcf
直接对vcf.gz文件进行注释:
cmdbtools annotate -i multiple_samples.vcf.gz > multiple_samples_CMDB.vcf
你可以的到如下的结果:
##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##reference=file:///home/tools/hg19_reference/ucsc.hg19.fasta
##INFO=<ID=CMDB_AN,Number=1,Type=Integer,Description="Number of Alleles in Samples with Coverage from CMDB_hg19_v1.0">
##INFO=<ID=CMDB_AC,Number=A,Type=Integer,Description="Alternate Allele Counts in Samples with Coverage from CMDB_hg19_v1.0">
##INFO=<ID=CMDB_AF,Number=A,Type=Float,Description="Alternate Allele Frequencies from CMDB_hg19_v1.0">
##INFO=<ID=CMDB_FILTER,Number=A,Type=Float,Description="Filter from CMDB_hg19_v1.0">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr21 9413612 . C T 6906.62 . AC=25;AF=0.313;AN=80;BaseQRankSum=0.425;CMDB_AC=2459;CMDB_AF=0.207525;CMDB_AN=11834;CMDB_FILTER=PASS
chr21 9413629 . C T 8028.88 . AC=30;AF=0.375;AN=80;BaseQRankSum=-1.200e+00;CMDB_AC=6906;CMDB_AF=0.305445;CMDB_AN=22406;CMDB_FILTER=PASS
chr21 9413700 . G A 7723.82 . AC=30;AF=0.375;AN=80;BaseQRankSum=-9.000e-02
chr21 9413735 . C A 10121.72 . AC=35;AF=0.438;AN=80;BaseQRankSum=0.977;CMDB_AC=2385;CMDB_AF=0.283965;CMDB_AN=8382;CMDB_FILTER=PASS
chr21 9413839 . C T 8192.08 . AC=28;AF=0.350;AN=80;BaseQRankSum=-5.200e-02
chr21 9413840 . C A 11514.35 . AC=38;AF=0.475;AN=80;BaseQRankSum=0.253
chr21 9413870 . T C 7390.60 . AC=26;AF=0.325;AN=80;BaseQRankSum=-4.270e-01
chr21 9413880 . T A 146.96 . AC=1;AF=0.013;AN=80;BaseQRankSum=2.12;ClippingRankSum=0.00
chr21 9413909 . G A 1131.78 . AC=10;AF=0.125;AN=80;BaseQRankSum=0.549;CMDB_AC=209;CMDB_AF=0.01507;CMDB_AN=13683;CMDB_FILTER=PASS
chr21 9413913 . C T 8120.65 . AC=28;AF=0.350;AN=80;BaseQRankSum=-4.390e-01;CMDB_AC=2870;CMDB_AF=0.205597;CMDB_AN=13955;CMDB_FILTER=PASS
chr21 9413945 . T C 43787.68 . AC=71;AF=0.888;AN=80;BaseQRankSum=0.089
chr21 9413995 . C T 9632.44 . AC=29;AF=0.363;AN=80;BaseQRankSum=0.747
chr21 9413996 . A G 41996.48 . AC=71;AF=0.888;AN=80;BaseQRankSum=-1.242e+00;CMDB_AC=3308;CMDB_AF=0.688533;CMDB_AN=4790;CMDB_FILTER=PASS
chr21 9414003 . T C 4256.54 . AC=19;AF=0.238;AN=80;BaseQRankSum=-6.030e-01
结果说明:
CMDB_AF: CMDB数据库中的突变频率信息;
CMDB_AN: 该位点在CMDB数据库中总的群体覆盖深度;
CMDB_AC: 该位点在CMDB数据库中支持该变异的群体覆盖深度;
CMDB_FILTER:质控标记,一般是PASS
1.2.3 登出
cmdbtool logout