Extract target region sequence with samtools but the output contains suquence exceeding the bed region

Question

[xusijiamed]

Hi, guys. I'm using "samtools view" to look at a sorted.bam. I tired setting a region

1. Using a bed file
2. Input the region in samtools command manually

(1）using a bed file

$ cat Gene.bed
chr19   11089362    11133830

$ samtools view -L Gene.bed [sorted.bam] | head

(2）input the region manually

$ samtools view [sorted.bam] "chr19:11089362-11133830" | head

Both methods gave me the sequence starts before "11089362"

b758e43b-3975-4d6e-a112-4e457161770a    0   chr19   **11089173**    60 5S43M1D181M2D9M6D185M3D49M3D13M1I2M3 ....

I'm confused. Could any one help me with this? Thank you very much!

[ATpoint]

Please show the output of head

[i.sudbery]

Edited for formatting

[wuzj42]

"5S43M1D181M2D9M6D185M3D49M3D13M1I2M3" ~ 500bp By the way, you should notice that bed file is 0-based half-open but region argument for samtools should be 1-based inclusive.

Answer 1

[i.sudbery]

When you ask samtools to output reads from a region, it outputs all reads that overlap that region. The read you show starts before 11,089,362, but finishes after it, thus the read overlaps with the region you specified.