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Problem to Understand the visualization of IGV

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? Untitled_2

igv visualization dna sequence
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updated by Devon Ryan Devon Ryan • written by saadleeshehreen saadleeshehreen

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

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written by Tm Tm

Does your BAM file have read groups?

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written by Devon Ryan Devon Ryan

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'?

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written by saadleeshehreen saadleeshehreen

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.

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written by Devon Ryan Devon Ryan

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