How to convert bam to fasta
0
0
Entering edit mode
10 months 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 • 378 views
ADD COMMENT
1
Entering edit mode

Since you have special type of data (ddRAD) just wanted to make sure that you are aware of stacks (LINK).

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Thanks for your reply.

Would you mind sharing the commands for the same?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.**

ADD REPLY

Login before adding your answer.

Traffic: 1274 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6