Samtools mpileup refrence fasta file input

Question

[cvu]

I'm using Samtools mpileup to convert my sorted.bam file to .bcf files. i've used multiple refrences to align my paired end reads. I've used GRCh38_Chr1 and GRCh38_Chr10.

samtools mpileup -g -f ref.fna aligned.sorted.bam > sim_variants.bcf

In above argument, how do i mention multiple reference fasta files ?

Answer 1

[Devon Ryan]

Just concatenate the files and use that.

[cvu]

okay . thanks Devon Ryan !!