What are files generated by bwa

[prasadg]

Hell everyone,

I am just starting with bwa. I have no clue what does .ann .pac . amb .bwt
means. I am trying to map reference fasta database of maize with given samples.

please help!!

[swbarnes2]

Hell everyone,

I am just starting with bwa. I have no clue what does .ann .pac . amb .bwt
means. I am trying to map reference fasta database of maize with given samples.

please help!!

Don't worry about them. They are files that makeup the reference index. It's the reference sequence transformed so that the short mapping can be carried out very quickly.

[prasadg]

Don't worry about them. They are files that makeup the reference index. It's the reference sequence transformed so that the short mapping can be carried out very quickly.

Thanks ..

I have one more question.
I am trying to map difference sequences with reference fasta database. I have generated the different sam files by tweaking the paramaters of bwa in 'aln'.
Now I want to compare those sam files . Compare of sam files is basically How many hits i got for perticular reference. How should I do this ?

[swbarnes2]

Thanks ..

I have one more question.
I am trying to map difference sequences with reference fasta database. I have generated the different sam files by tweaking the paramaters of bwa in 'aln'.
Now I want to compare those sam files . Compare of sam files is basically How many hits i got for perticular reference. How should I do this ?

Samtools.

convert your .sams to .bam (you really should always pipe bwa sampe/sampe into samtools to convert on the fly. .sam files are stupidly and pointlessly large.

So, convert your .sam to .bam, sort the .bam, index it, and run samtools idxstats.

[prasadg]

Samtools.

convert your .sams to .bam (you really should always pipe bwa sampe/sampe into samtools to convert on the fly. .sam files are stupidly and pointlessly large.

So, convert your .sam to .bam, sort the .bam, index it, and run samtools idxstats.

Thanks alot for your reply.

But this is the problem I am facing when I m tring to convert sam to bam using samtools

/bwa/new$ samtools view -b -S 12.sam > 1.bam
[samopen] SAM header is present: 315121 sequences.