consensus sequence calling

Question

[G.S]

Hi all,

I would like to call the consensus sequence for my virus sequence. I have tried this command but I am getting empty seq_89.vcf.gz output

Here is the command I used:

Generate your bam file as usual

samtools sort -@ 56 seq-89-highquality.bam -o seq-89-highquality.sorted.bam 


bcftools mpileup -Ou -f KT992094.1.fasta seq-89-highquality.sorted.bam --threads 56 --annotate FORMAT/AD,INFO/AD | bcftools call -mv -Oz --ploidy 2 --threads 56 > seq_89.vcf.gz 

Any help would be much appreciated and thanks in advance

Answer 1

[bk11]

Please check out these posts Generating consensus sequence from bam file