Getting consensus fasta sequence for a chromosome from a bam file

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5.6 years ago

nagarsaggi ▴ 40

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

alignment • 1.5k views

ADD COMMENT • link updated 5.6 years ago by finswimmer 16k • written 5.6 years ago by nagarsaggi ▴ 40

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So essentially what you need is to get a single chromosome from the bam file? Have you looked at the manual of samtools?

ADD REPLY • link 5.6 years ago by WouterDeCoster 47k

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