diff --git a/README.md b/README.md index eaa489b..0816833 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ It is an `R` package to make a pseudo reference genome subsituted with the SNP variants of given samples. -## Installation +## Installation (< 10 mins) Install [devtools](https://github.com/hadley/devtools) first, and then use devtools to install `pseudoRef` from github. ``` devtools::install_github("yangjl/pseudoRef") @@ -50,13 +50,6 @@ Before running the package, we should use `BCFtools` to convert VCF/BCF file int # bcftools query -f 'chr\tpos\tref\talt[\t%SAMPLE]\n' JRI20_bi_snps_annot.vcf.gz > JRI20_bi_snps_annot.header ``` -## TODO -1. add `test` data. -2. write a help document and real usage examples. -3. report a more reasonable substitution statistics. -4. visulize the report. -5. handle indels. - ## License This package is free and open source software, licensed under GPL.