Samtools mpileup - how to define the region (I am lost!)

TabeaK · 11-29-2012, 11:37 AM

Hi everyone!

After busily mapping my tons of reads and generating and merging BAM files I have reached the next level of confusion...

I wanna try some consensus/SNP calling; but only for a region (using the -r option); or in my case; a scaffold.

My ref genome is the result of a shotgun assembly and contains various scaffolds.

They are named as follows (as an example):

gi|123456789|ref|NW_123456789.1|

The 123456789 are just models of course...how the hell do I select one of the scaffolds as a region?

No matter what I put in, I get the wrong scaffold (always the first in the genome) as output... or I get BAM parsing errors!

maubp · 11-29-2012, 01:49 PM

The pipe characters (vertical bars) may need to be escaped (written as \| or slash pipe) or the region argument enclosed in quotes - otherwise the pipe symbol has the meaning at the command line of piping to the next command.

Perhaps you could show us an actual example copy and pasted from your terminal?

TabeaK · 11-29-2012, 02:17 PM

OMG!

Of course! That is such a simple thing...I need to go to bed.

Thank you so much maubp!

Enclosing the entire scaffold name in "" worked like a charm!

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11-29-2012, 11:37 AM	#1
TabeaK Member Location: Germany Join Date: Oct 2012 Posts: 48	Samtools mpileup - how to define the region (I am lost!) Hi everyone! After busily mapping my tons of reads and generating and merging BAM files I have reached the next level of confusion... I wanna try some consensus/SNP calling; but only for a region (using the -r option); or in my case; a scaffold. My ref genome is the result of a shotgun assembly and contains various scaffolds. They are named as follows (as an example): gi\|123456789\|ref\|NW_123456789.1\| The 123456789 are just models of course...how the hell do I select one of the scaffolds as a region? No matter what I put in, I get the wrong scaffold (always the first in the genome) as output... or I get BAM parsing errors!

11-29-2012, 01:49 PM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	The pipe characters (vertical bars) may need to be escaped (written as \\| or slash pipe) or the region argument enclosed in quotes - otherwise the pipe symbol has the meaning at the command line of piping to the next command. Perhaps you could show us an actual example copy and pasted from your terminal?

11-29-2012, 02:17 PM	#3
TabeaK Member Location: Germany Join Date: Oct 2012 Posts: 48	OMG! Of course! That is such a simple thing...I need to go to bed. Thank you so much maubp! Enclosing the entire scaffold name in "" worked like a charm!