IGV calling wrong mismatches

[François Kroll]

I keep on having examples of that... It seems like IGV is calling mismatches that are not correct.

I am attaching an screenshot of an example. "Show mismatched bases" is turned on, and IGV is colouring the very first nucleotide (C) to the right, while the reference does seem to be C too.

I am aligning and visualising to hg38 and I am using IGV 2.4.10.

Can someone help?

[James Robinson]

Do you have "show soft clips" turned on?

Could you supply some sample data.   You can export that alignment directly from IGV,  right click and select "export alignments"

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[François Kroll]

I do have "Show soft-clipped bases" turned on. But I don't see why these should be clipped in the first place?

Here is an example file (.bam + .bai) where it happens. Look for position chr20:4693700 (hg38), it is colouring the 5' TCC as mismatches while they are not.

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[James Robinson]

Did you check to see if the base in your example ("C") is soft-clipped?  Soft-clipped bases are considered by definition to be mismatched as they are not part of the alignment.

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[James Robinson]

The TCC is indeed soft clipped, so this is normal.   The question of why it is soft-clipped is of course for your aligner.