Question: BAM/SAM to FASTA conversion
1
gravatar for biolab
3.1 years ago by
biolab980
biolab980 wrote:

Hi everone,

I searched Biostars for BAM/SAM to FASTA conversion method, and found the tools EMBOSS Picard could do this (Convert Bam File To Fasta File)   I am wondering is there any perl script to complish this work?   I should note that my seq data is strand-specific seq, so the command samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' may not be very good.

I appreciate any of your solutions. Thanks a lot!

sam bam • 17k views
ADD COMMENTlink modified 23 days ago by GenoMax42k • written 3.1 years ago by biolab980
2
gravatar for Chadi Saad
7 months ago by
Chadi Saad40
France
Chadi Saad40 wrote:

you need to add '-' fot seqtk in order to read from pipe :

samtools bam2fq input.bam | seqtk seq -A - > output.fa
ADD COMMENTlink modified 7 months ago • written 7 months ago by Chadi Saad40

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

ADD REPLYlink written 7 months ago by WouterDeCoster26k
10
gravatar for Istvan Albert
3.1 years ago by
Istvan Albert ♦♦ 75k
University Park, USA
Istvan Albert ♦♦ 75k wrote:

The advice in the post you link to is greatly outdated. One of the reasons we should revisit these posts. There are far easier/faster ways to accomplish the same task.

The latest versions of samtools have the bam2fq command. Chain that to seqtk seq like so:

samtools bam2fq input.bam | seqtk seq -A > output.fa
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Istvan Albert ♦♦ 75k

Hi Istvan, thank you very much for your answer.  It's much helpful for my work.  I just have two more minor questions: (1) my samtools version is Version: 0.1.8 (r613).  I did not see samtools bam2fq function, so I need to update samtools?  (2) Additionally is seqtk inside samtools? If not, where to get it?  Thanks a lot!

ADD REPLYlink written 3.1 years ago by biolab980
1

You need to update samtools to at least 1.1 http://www.htslib.org/

Get seqtk from https://github.com/lh3/seqtk see also  How To Obtain And Install Seqtk

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 75k

Hi Istvan, your answer is really helpful.

ADD REPLYlink written 3.0 years ago by biolab980
3
gravatar for Carambakaracho
24 days ago by
Switzerland
Carambakaracho40 wrote:

For future record: samtools versions >1.3 can convert bam to fasta directly via samtools fasta

samtools --help

Program: samtools (Tools for alignments in the SAM format)
Version: 1.4 (using htslib 1.4)

Usage:   samtools <command> [options]

Commands:
  [...]
  -- File operations
     [...]
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA
  [...]
ADD COMMENTlink written 24 days ago by Carambakaracho40
0
gravatar for Alex Reynolds
24 days ago by
Alex Reynolds22k
Seattle, WA USA
Alex Reynolds22k wrote:

Via bam2bed and bed2faidxsta.pl:

$ bam2bed < reads.bam | bed2faidxsta.pl > reads.fa

Or sam2bed:

$ sam2bed < reads.sam | bed2faidxsta.pl > reads.fa
ADD COMMENTlink modified 24 days ago • written 24 days ago by Alex Reynolds22k
0
gravatar for GenoMax
23 days ago by
GenoMax42k
United States
GenoMax42k wrote:

reformat.sh from BBMap suite will do the conversion efficiently.

reformat.sh in=your.bam out=seq.fa
reformat.sh in=your.sam out=seq.fa
ADD COMMENTlink modified 23 days ago • written 23 days ago by GenoMax42k
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