GDBIGtools: A command line tools for GDBIG varaints browser

Overview

GDBIGtools: A command line tools for GDBIG varaints browser

PyPI Version License

Introduction

Born in Guangzhou Cohort Study Genome Research Database is based on thousands of trios families recruited by the BIGCS Project to conduct whole-genome-sequencing, genome variation detection, annotation and analysis.Phase I included 332 parent-child trios’ families, 1392 mother-child sample pairs, 14 father-child sample pairs, and 70 unrelated children, 150 adult females, and 25 adult males, for a total of 4053 individual samples.The GDBIG delivers periodical and useful variation information and scientific insights derived from the analysis of thousands of born in Guangzhou China sequencing data. The results aim to promote genetic research and precision medicine actions in China.The delivering information includes any of detected variants and the corresponding allele frequency, annotation, frequency comparison to the global populations from existing databases, etc.

The Genome variation Database of BIGCS(GDBIG) is a large-scale Chinese genomics database produced by BIGCS and hosted in the Guangzhou Women and Children' Medicine Center. The GDBIG delivers peridical and useful variation information and scientific insights derived from the analysis of thousands of Chinese sequencing data. The results aim to promote genetic research and precision medicine actions in China.

The delivering information includes any of detected variants and the corresponding allele frequency, annotation, frequency comparison to the global populations from existing databases, etc.

GDBIGtools is a command line tool for this GDBIG variants browser.

Quick start

GDBIG variant browser allows authorized access its data through an Genomics API and GDBIGtools is a convenient command line tools for this purpose.

Installation

Install the released version by pip (Only support Python3 since v1.0.1):

pip install GDBIGtools

Please enable your API access from Profile in GDBIG browser before using GDBIGtools.

Help

type GDBIGtools -h/--help for detail.

Usage: GDBIGtools [OPTIONS] COMMAND [ARGS]...

Options:
  -h, --help  Show this message and exit.

Commands:
  annotate   Annotate input VCF file with BIGCS allele Frequency.
  login      Login GDBIG.
  logout     Logout GDBIG.
  print-api  Display API information for GDBIG.
  query      Query variants from GDBIG database.

Login

Login with GDBIGtools by using GDBIG API access key, which could be found from if you have apply for it.

GDBIG_genomics_api

GDBIGtools login -k api-key -s api-secret-key

If everything goes smoothly, means you can use GDBIG as one of your varaints database in command line mode.

Logout

Logout GDBIGtools by simply run the command below:

GDBIGtools logout

Query a single variant

Variants could be retrieved from GDBIG by using query.

Run GDBIGtools query -h/--help to see all available options. There're two different ways to retrive variants.

One is to use -s parameters for variants on command, the other way uses -l for input-file.

Here are examples for quering varaints on command.

GDBIGtools query -s rs117518546
GDBIGtools query -s 21:9662064
GDBIGtools query -s 22:10577666-10581518
GDBIGtools query -s ENST00000269305
GDBIGtools query -s MTHFR

and you will get something looks like below:

##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:/human_reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa #CHROM POS ID REF ALT QUAL FILTER INFO chr22 10577666 rs1491296197 CAT C . PASS GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0 ">
##fileformat=VCFv4.2
##FILTER=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##reference=file:/human_reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr22   10577666        rs1491296197    CAT     C       .       PASS    GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0

Quering for input-file.

A list of variants could be retrieved from GDBIG by using the parameters of -l when apply by query.

GDBIGtools query -l positions.list > result.vcf

Format for positions.list, could be a mixture of

  • rs ID
  • ensembl transcript ID
  • gene symbol and ensembl gene ID
  • chrom position and chrom start end, even with or without chr in the chromosome ID column
#search key words
rs117518546
chr1:11795125
ENST00000269305
MTHFR

#CHROM	POS	[POS_END]
chr22	17662883
22	17669209    17669357

result.vcf is VCF format and looks like below:

##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:/human_reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa #CHROM POS ID REF ALT QUAL FILTER INFO chr22 10577666 rs1491296197 CAT C . PASS GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0 chr22 10577851 . TA T . PASS GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0 chr22 10580900 . ATTC A . PASS GDBIG_AF=0.000369;GDBIG_AF_SouthChina=0.000506;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0 chr22 10581005 rs1268262722 C T . PASS GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0.003571;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0 chr22 10581404 rs1283129074 G A . PASS GDBIG_AF=0.059975;GDBIG_AF_SouthChina=0.060162;GDBIG_AF_CentralChina=0.061151;GDBIG_AF_EastChina=0.057566;GDBIG_AF_SouthwestChina=0.028571;GDBIG_AF_NortheastChina=0.081395;GDBIG_AF_NorthwestChina=0.075342;GDBIG_AF_NorthChina=0.07377 chr22 10581518 rs1318646482 T A . PASS GDBIG_AF=0.000739;GDBIG_AF_SouthChina=0.001011;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0 ">
##fileformat=VCFv4.2
##FILTER=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##reference=file:/human_reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr22   10577666        rs1491296197    CAT     C       .       PASS    GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0
chr22   10577851        .       TA      T       .       PASS    GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0
chr22   10580900        .       ATTC    A       .       PASS    GDBIG_AF=0.000369;GDBIG_AF_SouthChina=0.000506;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0
chr22   10581005        rs1268262722    C       T       .       PASS    GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0.003571;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0
chr22   10581404        rs1283129074    G       A       .       PASS    GDBIG_AF=0.059975;GDBIG_AF_SouthChina=0.060162;GDBIG_AF_CentralChina=0.061151;GDBIG_AF_EastChina=0.057566;GDBIG_AF_SouthwestChina=0.028571;GDBIG_AF_NortheastChina=0.081395;GDBIG_AF_NorthwestChina=0.075342;GDBIG_AF_NorthChina=0.07377
chr22   10581518        rs1318646482    T       A       .       PASS    GDBIG_AF=0.000739;GDBIG_AF_SouthChina=0.001011;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;GDBIG_AF_NorthwestChina=0;GDBIG_AF_NorthChina=0

Actrually you can use -s and -l simultaneously if you like. And positions.list could just contain one single position.

GDBIGtools query -s 22:46616520 -l positions.list > result.vcf

Annotate your VCF files

Annotate your VCF file with GDBIG by using GDBIGtools annotate command.

Download a list of example variants in VCF format from GDBIG.test.vcf. To annotate this list of variants with allele frequences from GDBIG, you can just run the following command in Linux or Mac OS.

GDBIGtools annotate -i GDBIG.test.vcf > output.GDBIG.test.vcf

It'll take about 2 or 3 minutes to complete 2,000+ variants' annotation. Then you will get 8 new fields with the information of GDBIG in VCF INFO:

  • GDBIG_AF: Alternate Allele Frequencies in GDBIG;
  • GDBIG_AF_SouthChina: Alternate Allele Frequencies from GDBIG in SouthChina region;
  • GDBIG_AF_CentralChina: Alternate Allele Frequencies from GDBIG in CentralChina region;
  • GDBIG_AF_EastChina: Alternate Allele Frequencies from GDBIG in EastChina region.
  • GDBIG_AF_SouthwestChina: Alternate Allele Frequencies from GDBIG in SouthwestChina region;
  • GDBIG_AF_NortheastChina: Alternate Allele Frequencies from GDBIG in NortheastChina region;
  • GDBIG_AF_NorthwestChina: Alternate Allele Frequencies from GDBIG in NorthwestChina region;
  • GDBIG_AF_NorthChina: Alternate Allele Frequencies from GDBIG in NorthChina region.
##FORMAT= ##FORMAT= ##FORMAT= ##bcftools_concatVersion=1.9+htslib-1.9 ##reference=file:/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO chr22 10515882 rs1490973086 G A . PASS GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_CentralChina=0.116307;GDBIG_AF_CentralChina=0.116307;GDBIG_AF_CentralChina=0.116307;GDBIG_AF_EastChina=0.113487;GDBIG_AF_EastChina=0.113487;GDBIG_AF_SouthwestChina=0.078571;GDBIG_AF_NortheastChina=0.098837;AR2=0.63;AR2=0.63 chr22 10516264 . TAC T . PASS GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0.001645;GDBIG_AF_EastChina=0.001645;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;AR2=0.78;AR2=0.78 chr22 10516615 rs1228174166 TTTG T . PASS GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;AR2=0.221;AR2=0.221 chr22 10518420 rs1177693979 CA C . PASS GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;AR2=0.547;AR2=0.547 ">
##fileformat=VCFv4.2
##FILTER=
##FORMAT=
##FORMAT=
##FORMAT=
##bcftools_concatVersion=1.9+htslib-1.9
##reference=file:/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr22   10515882        rs1490973086    G       A       .       PASS    GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF=0.105296;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_SouthChina=0.106336;GDBIG_AF_CentralChina=0.116307;GDBIG_AF_CentralChina=0.116307;GDBIG_AF_CentralChina=0.116307;GDBIG_AF_EastChina=0.113487;GDBIG_AF_EastChina=0.113487;GDBIG_AF_SouthwestChina=0.078571;GDBIG_AF_NortheastChina=0.098837;AR2=0.63;AR2=0.63
chr22   10516264        .       TAC     T       .       PASS    GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_SouthChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0.001645;GDBIG_AF_EastChina=0.001645;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;AR2=0.78;AR2=0.78
chr22   10516615        rs1228174166    TTTG    T       .       PASS    GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF=0.000123;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_SouthChina=0.000169;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;AR2=0.221;AR2=0.221
chr22   10518420        rs1177693979    CA      C       .       PASS    GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF=0.000246;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_SouthChina=0.000337;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_CentralChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_EastChina=0;GDBIG_AF_SouthwestChina=0;GDBIG_AF_NortheastChina=0;AR2=0.547;AR2=0.547

Citation

Issues
  • Master

    Master

    version 1.1.1 add the other database [CMDB, ChinaMAP, NyuWa, WBBC, gnomAD and 1000 genomes project] allele frequency information.

    opened by aiyacharley 0
Owner
广州市出生队列基因组学研究(The genomics study of BIGCS)
广州市出生队列基因组学研究(The genomics study of BIGCS)
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