wtsi-hpag/varibase

A pipeline to correct variation errors of SNPs/indles from genome assembly

varibase v1.0

This is the code to correct variation errors of SNPs/indles from genome assembly

You have a variation VCF file from GATK or samtools, but you want to change the bases in your reference sequence.

Download and Compile:

$ git clone  https://github.com/wtsi-hpag/varibase.git 
$ cd varibase 
$ make 

For SNP base change

egrep "DP=" var.flt.vcf | awk '((length($4)==1)&&(length($5)==1)){print $1,$2,$4,$5,$6}' > snp.dat ./varibase -snp 1 snp.dat input.fasta output.fasta

For indel base change

#egrep "DP=" var.flt.vcf | egrep INDEL | awk '{print $1,$2,$4,$5,$6}' > indel.dat ./varibase -indel 1 indel.dat input.fasta output.fasta

Indel length can be upto 1000bps

Note: please always do SNP corrections first and then indels.

Any problems, contact Zemin Ning ( zn1@sanger.ac.uk )