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  • Bam file to Consensus Fasta/fastq in python

    Hello!

    Summary:
    I want to get the same result as I get from this command, but in python (BioPython/Pysam):
    Code:
    samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
    Full story:
    I need to extract the consensus fasta from an aligned bam file, currently I'm doing it with samtools, but I'll be more than happy if I can implement it in python without 3rd party tools. That's important because this step is an intermediate step, so I need this fasta sequence to play with it.

    Thanks everyone for your help.

    Best,

    Daniel.

  • #2
    Can't you call these tools within your Python script? As long as machine you are running have the tools installed, it should be fine.

    Editing:
    Sorry, when read you message a second time, I realized that you said you do not want to use third party tools.
    Last edited by rnaeye; 05-17-2014, 11:01 AM. Reason: made mistake

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