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  • From bam to reference genome

    I have a WGS bam file and I would like te create a reference genome from it. Is this possible and any idea how to proceed? Coverage is 35x, Qual all above 40.

  • #2
    If the BAM file aligned against a reference then you could use samtools to create a new consensus sequence (from Samtools manual)

    Code:
    $ samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq

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