Extract aligned sequence coordinates from SAM or BAM file

[pirates.genome]

Hi,
I have a Illumina sequence reads which I mapped to HG19 using BWA. Resulting BAM file is indexed and sorted. Now what I want is to identify the region of alignment. Let me give an example, on chromosome 1 starting from base 1 to 10000, there are many reads aligned and then there is no any read aligned from 10000 to 20000 and then again from 20000 to 30000 there are many reads aligned and so on...

I want an output like
chr1 1 10000
chr1 20000 30000
etc...etc...

I searched for tools doing similar functions but didn't find anything.
Any help will be really appreciated.

Thanks.

[colindaven]

Have a look at a variation of:

samtools view -L bedfile.bed x.bam

[pirates.genome]

Thnx colindaven,

I looked into samtools view -L option but that is not what I am looking for.

Let me explain the problem,
I have targeted DNA sequencing data from Illumina. After aligning to reference using BWA I got BAM files. From BAM files I want to extract a continuous stretch of reference region to which multiple reads are aligned. Assume that reads are aligned in following way:
read1 aligned to chr1:1-50
read2 chr1:10-60
read3 chr1:30-80
read4 chr1:150-200
read5 chr1:200-250
read6 chr1:250-300
read7 chr1:350-400
and so on....

Now I want continuous stretch of reference to which any read is aligned. Output should be:
chr1:1-80
chr1:150-300
chr1:350-400
and so on...

This output tells us that there are several number of reads aligned to chr1 position 1 to 80 in continuation of each other and then no any read aligned to position 80 to 150 and so on...

Is there an easy way to do so..??..

Thanks.

[Richard Finney]

SIMPLE VERSION ... using samtools depth and awk ...
#ploc = previous location, pchr=previous chromsome
#Set SAMT and BAMF to samtools and your bamfile.
export SAMT=/h1/finneyr/samtools-0.1.18/samtools
export BAMF=98023.bam
$SAMT depth $BAMF | awk '{ if ($2!=(ploc+1)){if (ploc!=0){printf("%s %d-%d\n",$1,s,ploc);}s=$2} ploc=$2; }

More complicated version that handles chr1->chr2 transition and flushes at the end. (I think, this is not completely debugged and and is just a one-off. Not all corner conditions maybe addressed.)

$SAMT depth $BAMF | \
awk '
BEGIN{firsttime=1;}
{
if (pchr!=$1) { if (firsttime==1) { firsttime = 0;} else { printf("%s %d-%d\n",pchr,s,ploc);}s=$2}
else { if ($2!=(ploc+1)){if (ploc!=0){printf("%s %d-%d\n",$1,s,ploc);}s=$2} }
ploc=$2; pchr=$1
}
END{ printf("%s %d-%d\n",pchr,s,ploc);}
'
CAVEAT: samtools depth doesn't do cigar 'N' quite right so this won't work for RNA in the best way.

[pirates.genome]

SIMPLE VERSION ... using samtools depth and awk ...
#ploc = previous location, pchr=previous chromsome
#Set SAMT and BAMF to samtools and your bamfile.
export SAMT=/h1/finneyr/samtools-0.1.18/samtools
export BAMF=98023.bam
$SAMT depth $BAMF | awk '{ if ($2!=(ploc+1)){if (ploc!=0){printf("%s %d-%d\n",$1,s,ploc);}s=$2} ploc=$2; }

More complicated version that handles chr1->chr2 transition and flushes at the end. (I think, this is not completely debugged and and is just a one-off. Not all corner conditions maybe addressed.)

$SAMT depth $BAMF | \
awk '
BEGIN{firsttime=1;}
{
if (pchr!=$1) { if (firsttime==1) { firsttime = 0;} else { printf("%s %d-%d\n",pchr,s,ploc);}s=$2}
else { if ($2!=(ploc+1)){if (ploc!=0){printf("%s %d-%d\n",$1,s,ploc);}s=$2} }
ploc=$2; pchr=$1
}
END{ printf("%s %d-%d\n",pchr,s,ploc);}
'
CAVEAT: samtools depth doesn't do cigar 'N' quite right so this won't work for RNA in the best way.

Hi Richard Finney,
Thank you for very helpful code. First code worked good for me.

[ishmael]

I think BEDtools should also fit your demand.
1. convert the bam into bed by bam2bed
2. mergeBed.