How to convert bam to fasta
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3.8 years ago
rijithraj • 0

Can anyone suggest the best way to convert bam to fasta in an aligned format?

I have a data from ddRad sequencing. Initially, I want to count the number of restriction sites obtained. So, I already got suggestions to get it mapped to the genome and count the sites using available python code.

Following are the commands I have used for fasta conversion.

samtools mpileup -uf ref.fa aln.bam | bcftools call -mv -Oz -o calls.vcf.gz

tabix calls.vcf.gz

cat ref.fa | bcftools consensus calls.vcf.gz > cns.fa

Could you please have look at this and please tell me know if this is the right format where I could get a reliable number of restriction sites?

Other pipeline suggestions are also most welcome.

sequencing alignment next-gen • 1.6k views
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Since you have special type of data (ddRAD) just wanted to make sure that you are aware of stacks (LINK).

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Thank you for this information. The pipeline looks good to me. Let me have a check.

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You can convert your bam to bed then use bedtools getfasta to convert the bed to fasta.

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Thanks for your reply.

Would you mind sharing the commands for the same?

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Get bed with: bamTobed -i <bamfile> -o <bed_output_name>

Get fasta with: bedtools getfasta -fi <genome_file.fasta> -bed bed_output_name -o your_desired.fasta

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copy/pasted from https://www.htslib.org/doc/samtools-fasta.html:

**SYNOPSIS

samtools fastq [options] in.bam

samtools fasta [options] in.bam

DESCRIPTION

Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked. The files will be automatically compressed if the file names have a .gz or .bgzf extension.**

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