BWA - Samtools problem

[totalnew]

For samtools view ..., I don't see any sense you need to use it, since I normally use it to convert bam file back to sam file.

[totalnew]

Try these two commands:

>samtools pileup -cf ref.fa testing.bam
or
>samtools pileup -cf ref.fa -t ref.fa.fai testing.sam

They are actually the same, but you would have to get bam file first which will require the indexed reference sequence (use faidx option to get it).

[nilshomer]

Hello everyone

There are some topics concerning BWA and Samtools, but i still haven't found the solution to my problem...

Ok, here is what i do

1. I run BWA aln and I get a .sai file
2. I run BWA samse and I get a .sam file

So far so good.

But now i am having troubles using the 'pileup function'

As far as i understand i should use ./samtools -f ref.fna testing.sam

but it is giving me errors.

I am probably just using a wrong command or maybe i should convert the .sam file to a .bam file? I have tried this using:
samtools view -bt ref.fna -o out.bam testing.sam:sam_header_read2: Assertion `fp' failed.
samtools view -b ref.fna -o out.bam testing.sam:segmentation error

Anyone has the exact commando for me to got from BWA to 'pileup results' in samtools?

thx

If you have a "sam" file, then you must use the "-S" flag (for the input is SAM) with "samtools view". "samtools view" expects a ".bam" file, so you could also convert it to a BAM file.

[joa_ds]

Hello everyone

There are some topics concerning BWA and Samtools, but i still haven't found the solution to my problem...

Ok, here is what i do

1. I run BWA aln and I get a .sai file
2. I run BWA samse and I get a .sam file

So far so good.

But now i am having troubles using the 'pileup function'

As far as i understand i should use ./samtools -f ref.fna testing.sam

but it is giving me errors.

I am probably just using a wrong command or maybe i should convert the .sam file to a .bam file? I have tried this using:
samtools view -bt ref.fna -o out.bam testing.sam:sam_header_read2: Assertion `fp' failed.
samtools view -b ref.fna -o out.bam testing.sam:segmentation error

Anyone has the exact commando for me to got from BWA to 'pileup results' in samtools?

thx