And finally the BAM file to the SAM file, example.sam
And we're going to send that in to a file.
Thats example.sam.bam.
So that we dont override the example of the bam.
So that's a conversion operation. And to make sure that they're succeeding we're going to
take a look at the file samtools view example.sam.bam.
Or we could also run flag stats to make sure that we have
the same number of records as in the original file.
So, that was really the second type of function
which was to convert from the BAM format and to SAM and
conversely from the SAM format to the BAM format.
And next I am going to illustrate how we can use
SAMtools with the command view in order to extract alignments within a range.
So let's say that we're interested in just looking at alignments on chromosome 22 between
location 24 million and location 25 million. And how will we do that?
We can actually do it two ways. So let me remind you of the command samtools1 view.
You probably have noticed
that we have sam tools view, options input bam.
And then there's an optional parameter at the end
that allows us to specify the region. So that's one way.
But we can also specify especially if we have multiple search regions on the genome,
we can also specify the input regions in a file in for instance in BED format.
Dash L, so with the dash L only includes reads overlapping these BED file.
which will contain intervals. So let's try both options.
So in the first option,
we just type samtools1 view,
will give the alignment file example.bam and then the range chromosome 22,
24 million to 25 million.
So, let's see what happens.
So notice that 'm simplifying to use example.bam.
Oh and it then tells me that my file has to be indexed.
Now normally a file in order to be indexed,
has to be sorted.
But in this case if we're looking at our alignment file,
samtools, view example.bam and put it only at the header line.
We don't need more than that.
You are going see that the file is already sorted by coordinates.
So we can simply apply the index just like we have
demonstrated in the previous section samtool1,
index example.bam And this creating the file example.bam.bai
And now we can proceed with our range extraction,
samtools view example.bam and then we are giving it the range.
Then now, we can actually apply the same set of parameters
to specify the type of the output.
In this case the output will be in the SAM format.
So let's look at what it looks like.
One option will be with head.
So you will notice that this are alignments and the start position is following position
24 million and let's
also use tail to look at the last lines and make sure that they are also
within the range that we asked for.
So indeed the start position for the last alignments in the file.
All alignments being sorted by their coordinates.
So the last one is 24 million, nine hundred seventy one and so on.
So just a little bit shorter than 25 million boundary.
So, this shows one of the algorithms which
we can use samtools view to extract alignments within a range.
And let's try the next one.
For this purpose, I have created a file,
that's example.bed.
It contains just one line.
You might recall from the BED format that it requires at least columns.
The chromosome number,
start position and then end position interval.
And I only have one interval here but then we have multiple lines.
So let's now perform the same operation, samtools1 view,
dash Capital L which says,
extract only alignments within a range.
And the range is specified by the example.bed file and then
we don't need this region in here.
