Adding coverage data to your VCF

Adding coverage data to your VCF

pVACseq is able to parse coverage information directly from the VCF. The expected annotation format is outlined below.
pvacseq能够解析你的覆盖信息从你的ＶＣＦ文件中.
有些

Using the vcf-readcount-annotator to add coverage information to your VCF.

Some variant callers will already have added coverage information to your VCF. However, if your VCF doesn’t contain coverage information or if you need to add coverage information for additional samples or for RNA-seq data, you can use the vcf-readcount-annotator to do so.

The vcf-readcount-annotator will take the output from bam-readcount and use it to add readcounts to your VCF.

bam-readcount needs to be run separately for snvs and indels so it is recommended to first split multi-allelic sites by using a tool such as vt decompose.

Installing vt

 #this will create a directory named vt in the directory you cloned the repository
 1. git clone https://github.com/atks/vt.git  
 #change directory to vt
 2. cd vt