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carrier and trio analysis

Project description

vcf_split.py拆分注释后的vcf文件,结果文件`samplename.SNP OR INDEL.annovar.filter.csv`和`samplename.SNP OR INDEL.annovar.withoutfilter.csv`

inh_gene_phenotype.json,{gene:[inheritance,phenotype]},获得对应gene的遗传方式和表型 omim_gene.json,根据hpo号得到omim表型号,再根据omim表型号得到gene 家系样品需要先trio.py运行,annovar注释,再pedigree.py拆分(vcf必须仅有三人家系样本) 需要用到的模块: annotation_filter.py:变异过滤 hg38Tohg19.py:hg38坐标转成hg19坐标 hgvs.py:修改AAChange.refGene栏中碱基替换的格式,如果是插入缺失则不改变,仅输出转录本号数值最小的那个 database_format.py,对genemap2.txt 和omimdata.xlsx进行处理得到inh_gene_phenotype.json和omim_gene.json 如果有必要的话需要复制到~/soft/python/bin

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