BAM/SAM to Fasta

[Canadian_philosophy]

Hi there,

I have a couple of aligned sequences from BWA. I used samtools to get the BAM format. What I really need is the Fasta format of these aligned sequences. Is there a program that would help?

Thanks.

[maubp]

Yes, several, including one line shell scripts.

Possibly seqret from EMBOSS 6.3.x will do what you want.

See also this thread for SAM/BAM to FASTQ which is very relevant:

http://seqanswers.com/forums/showthread.php?t=6164

[Canadian_philosophy]

Thanks Maubp, I just downloaded Emboss. I will get back if I bump into trouble.
Thanks very much.

[olus]

This one liner would give you a fasta formatted file from a bam alignment:

samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta

Hope this helps.

Gabriel

[ulz_peter]

Or picard SamToFastq:

Works with BAM Files as well and supports some other options:

http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq

[tejaminnu]

Hi Gabriel,

Is there a way to do the opposite ? What i mean is that, i have a file called mrna_ref.fa (fasta file), can i convert it into a sam or a bam file using Samtools in the command line.

Regards
Teja

[olus]

Hi Teja.
In theory you can convert a multifasta file in a sam (tabular) file, and then convert to bam with samtools view -b.
But the fasta file only contains information on the nucletide sequence itself, nothing about the mapping, read quality etc... which are indeed the columns of the sam file (you will also need to rebuild the sam header).
In conclusion I think it's useless to convert a fasta file into a sam file, but I can't exclude that you are dealing with something that requires such conversion.
Would please briefly explain your case?

Thank you.

Best regards.
Gabriel

[tejaminnu]

Hi

Hi Gabriel,

I want to send u the file. which is very small. Probably u can have a look at it .. Can u just send me a mail to this id, if its not a problem.

[email protected]

Regards
Teja

[tejaminnu]

Basically i have a Stand Alone Blast program running. The "fasta" file served as a reference file using which i blasted the large database file that i had. I am trying to find out if i can call SNP's using "Blast" program.

And i want to confirm it by getting the SNP's using Samtools.

Is the above explanation even valid. ?

Do let me know

Regards
Teja

[tejaminnu]

Hi Gabriel,

I want to send u the file. which is very small. Probably u can have a look at it .. Can u just send me a mail to this id, if its not a problem.

[email protected]

Basically i have a Stand Alone Blast program running. The "fasta" file served as a reference file using which i blasted the large database file that i had. I am trying to find out if i can call SNP's using "Blast" program.

And i want to confirm it by getting the SNP's using Samtools.

Is the above explanation even valid. ?

Do let me know


Regards
Teja

[olus]

Hi Gabriel,

I want to send u the file. which is very small. Probably u can have a look at it .. Can u just send me a mail to this id, if its not a problem.

[email protected]

Basically i have a Stand Alone Blast program running. The "fasta" file served as a reference file using which i blasted the large database file that i had. I am trying to find out if i can call SNP's using "Blast" program.

And i want to confirm it by getting the SNP's using Samtools.

Is the above explanation even valid. ?

Do let me know


Regards
Teja

Hi.
If I understand it right, you have to:
1) align your fasta query file (mrna_fa) to a reference with blast
2) parse the blast output to be compliant with sam
3) use samtools to call SNPs (to a properly indexed reference)

for point 2) you can look at here:

http://seqanswers.com/forums/showthread.php?t=3759

In general I can say that blast it's not suited for efficient SNP calling , but I may be wrong.

Gabriel