BGI-lowpass imputation vcf stats
usage: java -jar vcfstats.jar [-d <FILE>] [-h] -i <FILE> [-o <String>] [-q <Float>]
Options:
-d,--dbsnp <FILE> dbsnp file(.vcf.gz), must be indexed [null]
-h,--help Print this help.
-i,--input <FILE> input file(VCF). [request]
-o,--output <String> report outdir [request]
| 指标 | 说明 |
|---|---|
| Failed Filters | 未通过质控的变异条目数 |
| Passed Filters | 通过质控的变异条目数 |
| SNPs | SNP类型变异条目数 |
| Insertions | Insertion类型变异条目数 |
| Deletions | Deletion类型变异条目数 |
| Same as reference | 未变异条目数(homref) |
| Missing Genotype | 缺失genotype信息(因质量过低过滤掉) |
| SNP Transitions/Transversions | 转换颠换比 |
| Total Het/Hom ratio | 杂合纯合比 |
| SNP Het/Hom ratio | SNP类型杂合纯合比 |
| Insertion Het/Hom ratio | Insertion类型杂合纯合比 |
| Deletion Het/Hom ratio | Deletion类型杂合纯合比 |
| Insertion/Deletion ratio | Insertion类型变异和Deletion类型变异比例 |
| Indel/SNP ratio | Indel和SNP类型变异比例 |
| max_GP >=0.8 ratio | GP值>=0.8的变异条目比例 |
| max_GP >=0.9 ratio | GP值>=0.9的变异条目比例 |