Create .bed file from Genbank file

[ksw9]

Hi,
I am trying to generate a .bed file of coordinates for a list of genes of interest so that I can extract reads from those regions from .bam files I have generated. Is there a tool for extracting coordinates and generating a .bed file from an annotated Genbank file?

Thank you,

[GenoMax]

A google search found this: https://gist.github.com/brantfaircloth/893580

[ksw9]

Great, thank you!
A related question: Is there a tool to generate .fasta consensus sequences from specific regions of interest? For example, I have a .bam file of all sample reads from which I extract reads of interest with bedtools intersect to create another .bam file. Then, I can use bedtools bamtofastq to generate a .fastq file of the regions of interest, but to then generate a .fasta consensus sequence, I do not want a .fasta covering the entire reference genome, but only the region indicated by the .bed file. Is there a tool for this?

[GenoMax]

Great, thank you!
A related question: Is there a tool to generate .fasta consensus sequences from specific regions of interest? For example, I have a .bam file of all sample reads from which I extract reads of interest with bedtools intersect to create another .bam file. Then, I can use bedtools bamtofastq to generate a .fastq file of the regions of interest, but to then generate a .fasta consensus sequence, I do not want a .fasta covering the entire reference genome, but only the region indicated by the .bed file. Is there a tool for this?

Try this to generate a consensus sequence from your genes of interest:

samtools mpileup -uf ref.fa -l your_bed_file aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

Then use seqtk to convert from fastq to fasta.

[ksw9]

Thanks, just what I was looking for!