Problem to Understand the visualization of IGV

Question

[saadleeshehreen]

I use BWA to create a bam file and visualize the alignment with IGV. I didn't split the window. But I get two alignments exact at the position of my gene of interest. What does it mean?

[Tm]

Can you highlight the portion which you are looking for in the image?

[saadleeshehreen]

red one ...

[Devon Ryan]

Does your BAM file have read groups?

[saadleeshehreen]

Its my first time I am working with IGV , BWA and samtools. I tried the same procedure with other genome and didn't see such alignment there. That seems quite normal. I don't know what happens with it. What do you mean by 'read groups'?

[Devon Ryan]

In situations where you might want to do variant calling you end up needing to merge multiple biological samples together in 1 BAM file. You can then label each alignment in that file to designate the sample it came from. These labels are call "read groups". My expectation is that this BAM file has read groups in it. You can see that by posting the output of samtools view -H your_file.bam | tail.