This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting consensus fasta sequence for a chromosome from a bam file

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
• 1,876 views • link
updated by finswimmer finswimmer • written by nagarsaggi • nagarsaggi

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

• 1 views • link
written by WouterDeCoster WouterDeCoster

0 answers

No answers yet.

Log in to answer this question.

More posts like this