I'm using samtools to extract some regions from a BAM file, and in some situations, I don't get back all of the reads that overlap the region.
For example:
Looking for all reads that overlap the region 2L:1376266-1376270 from this bam file (61MB). Using this command:
samtools view 801.2L.bam 2L:1376266-1376270
Samtools finds these these 14 reads with the command. However, looking at the area around that region (here's a slightly bigger area), I can see several more reads that overlap this region that aren't printed out by samtools.
The samtools view --region appears to work fine for most other regions in the file; only a small minority exhibit this behaviour.
Is this a bug in samtools, or am I missing something?
For example:
Looking for all reads that overlap the region 2L:1376266-1376270 from this bam file (61MB). Using this command:
samtools view 801.2L.bam 2L:1376266-1376270
Samtools finds these these 14 reads with the command. However, looking at the area around that region (here's a slightly bigger area), I can see several more reads that overlap this region that aren't printed out by samtools.
The samtools view --region appears to work fine for most other regions in the file; only a small minority exhibit this behaviour.
Is this a bug in samtools, or am I missing something?
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