I have a bam file per sample which I have generated by mapping Illumina short reads on ~1100 single copy orthologues genes (busco). I want to extract consense sequence from bam file for a given single copy orthologue, in another way for a given chromosome. The aim is to generate a multiple sequence alignment out of the consensus sequence of a particular single-copy ortholog gene.
Following command have been recommended for extracting consense from a bam file but I am not able to use it for a particular chromosome
samtools mpileup -uf reference.fa aligment.bam | bcftools view -cg - | vcfutils vcf2fq >out.fasta