SeqMinerCmd Tutorial

A command line tool for SeqMiner

(Updated October 1, 2013)

SeqMinerCmd is a convenient data extraction tools for VCF and BCF files. The software, SeqMinerCmd, can be downloaded in this link and its source code can be obtained from github.

This tutorial demonstrates by-region and by-gene based methods, and the extraction results can be stored as a R matrix or a list.

Extract gentoype matrix from VCF file

extract by region

./seqMiner -r "1:196621007-196634467" vcf/all.anno.filtered.extract.bcf.gz

## 1 region to be extracted.
## ----- 1:196621007-196634467 -----
## Position NA12286 NA12341 NA12342
## 1:196623337  1   2   0
## 1:196632129  0   2   0
## 1:196632470  1   2   0
## 1:196633606  2   2   2

extract by gene

./seqMiner --geneFile vcf/refFlat_hg19_6col.txt.gz -n CFH vcf/all.anno.filtered.extract.vcf.gz

## 1 region to be extracted.
## ----- CFH -----
## Position NA12286 NA12341 NA12342
## 1:196623337  1   2   0
## 1:196632129  0   2   0
## 1:196632470  1   2   0
## 1:196633606  2   2   2
## 1:196623337  1   2   0
## 1:196632129  0   2   0
## 1:196632470  1   2   0
## 1:196633606  2   2   2

Extract arbitrary fields from VCF file

extract by region

./seqMiner -r "1:196621007-196634467" -e CHROM,POS:DP:GT,GD vcf/all.anno.filtered.extract.vcf.gz

## CHROM    POS DP  NA12286:GD  NA12341:GD  NA12342:GD  NA12286:GT  NA12341:GT  NA12342:GT
## 1    196623337   23  0   2   21  0/1 1/1 0/0
## 1    196632129   25  1   7   17  0/0 1/1 0/0
## 1    196632470   28  3   7   18  0/1 1/1 0/0
## 1    196633606   26  2   5   19  1/1 1/1 1/1

extract by gene

./seqMiner --geneFile vcf/refFlat_hg19_6col.txt.gz -n CFH -e CHROM,POS:DP vcf/all.anno.filtered.extract.vcf.gz

## CHROM    POS DP
## 1    196623337   23
## 1    196632129   25
## 1    196632470   28
## 1    196633606   26
## 1    196623337   23
## 1    196632129   25
## 1    196632470   28
## 1    196633606   26

Contact

SeqMiner is developed by Xiaowei Zhan and Dajiang Liu. We welcome your questions and feedbacks.