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首页 / 国际千人基因组计划-1000genomes

国际千人基因组计划-1000genomes

罗大黑学生信 2021-07-28
2981

简介

            国际千人基因组计划，由中英美德等国科学家共同承担研究任务，旨在绘制迄今为止最详尽的、最有医学应用价值的人类基因组遗传多态性图谱。2012年11月大型国际科研合作项目“千人基因组计划”的研究人员在新一期英国期刊《自然》上发布了1092人的基因数据，这一成果将有助于更广泛地分析与疾病有关的基因变异。官网：

https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/

        1000genomes 数据库收录SNP 的相关信息， 其中包括：基因Symbol ID， 染色体区域，不同人群突变碱基的等位基因频率（alternative allele frequency）。

示例：rs=rs121434596 网址:

http://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000213281;r=1:115258244-115259244;t=ENST00000369535;v=rs121434596;vdb=variation;vf=642150019



软件注释

注释软件：annovar

注释软件调用的数据库：1000g2015aug (ALL.sites.2015_08 )

注释获取信息：1000基因组项目供选择的等位基因频率信息

执行命令：

table_annovar.pl  esp.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,EAS.sites.2015_09 -operation g,f -nastring .


>> cat esp.avinput 
1  11012  11012  C  G




>> cat myanno.hg19_multianno.txt
Chr  Start  End  Ref  Alt  Func.refGene  Gene.refGene  GeneDetail.refGene  ExonicFunc.refGene  AAChange.refGene  EAS.sites.2015_09
1  11012  11012  C  G  upstream  DDX11L1  .  .  .  0.0367


问题

执行过程遇到报错：

Argument "A" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 2.
Argument "T" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 3.
Argument "T" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 4.
Argument "T" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 5.
Argument "T" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 6.
Argument "A" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 7.
Argument "C" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 8.
Argument "G" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 9.
Argument "C" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 10.
Argument "C" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 11.
Argument "C" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 12.
Argument "CCGCCGTTGCAAAGGCGCGCCG" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 13.
Argument "CGCCGTTGCAAAGGCGCGCCG" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 14.
Argument "G" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 15.
Argument "C" isn't numeric in numeric eq (==) at /home/pipeline/helitec_pipeline/bin/annovar/annotate_variation.pl line 2461, <DB> line 16.
Done
-----------------------------------------------------------------
NOTICE: Multianno output file is written to myanno.hg19_multianno.txt
查阅代码后，发现应该数据库问题，少了一列 start (or end)；修改如下：
>> head hg19_EAS.sites.2015_08.txt
1  10177  A  0C  0.3363  rs367896724
1  10177  A  1AC  0.3363  rs367896724
1  10352  T  0A  0.4306  rs555500075
1  10352  T  1TA  0.4306  rs555500075
1  10542  C  T  0.001  rs572818783




>> awk '{print $1"\t"$2"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6}' hg19_EAS.sites.2015_08.txt > hg19_EAS.sites.2015_09.txt
>> head hg19_EAS.sites.2015_09.txt
1  10177  10177  A  0C  0.3363  rs367896724
1  10177  10177  A  1AC  0.3363  rs367896724
1  10352  10352  T  0A  0.4306  rs555500075
1  10352  10352  T  1TA  0.4306  rs555500075
1  10542  10542  C  T  0.001  rs572818783


数据库
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