Hello everyone! I want to get consensus sequence from my NGS data. I created sorted bam, and visualized it in IGV. I know that alligment has SNPs, insertions and deletions. After that I tried to get consensus sequence from my NGS data. I used two ways:
- From samtools manual: "Generate the consensus sequence for one diploid individual:
samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq" - this coomand gave me only SNPs in consensus sequence.
- Copy consensus sequence from IGV. It gave me consensus with SNPs and deletions.
How can I get insertions in consensus sequence?