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Follow the guide here: Generating consensus sequence from bam file
@genomax: I used that link before. but the problem is that in the vcf file I have both indels and SNPs and at some points they have overlap. in those regions program skips the indels (which is what I am interested in). do you have any solution for that
Split your VCF file by sample and then normalize it with a reference genome (
bcftools normorvt decompose+vt norm).A sample cannot have both an indel and an SNP at the same location.Note: If you're using
vt, decompose first, then split by sample and normalize at the end.EDIT: A sample can have an indel and an SNP at the same location, given they're both heterozygous and on different chromosomes. I'm not sure how that would translate to a consensus sequence.