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.
$ git clone https://github.com/wtsi-hpag/varibase.git
$ cd varibase
$ make
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
#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
Note: please always do SNP corrections first and then indels.
Any problems, contact Zemin Ning ( [email protected] )