Visualization of Frameshift mutations in IGV using Bam files

Question

[Maryam]

Hello,

I wanted to discuss frameshift mutations that difficult to interpret. I used both VCF file as well bam file to visualize them but I am unable to interpret what does bam or VCF telling me about that mutation.

e.g. in case of Bam file, IGV tells me that DEL 21 INS 6 G870(100%), T 0(0%)

Kindly can someone help me understanding such information? also if someone can explain the VCF information as well.

Thank you

Answer 1

[iraun]

Frameshift is a functional consequence of an insertion or a deletion, which creates an altered protein sequence with different amino acid content versus the reference protein (read here for more information). If you try to visualize a frameshift in IGV, you will only see the inserted or deleted nucleotides in the given position, and how many reads support that finding. Maybe uploading an screenshoot of what you need help with when visualizing the variant in IGV could help to have a more precise answer :).

You can find a lot of information regarding VCF format. You can always start with wikipedia. Basically each row in the VCF represents a variant position (unless you have a gVCF in which all the positions of the genome are listed) and the columns show different information, metrics, stats.. about the given variant.

[Maryam]

e.g. this is the frameshift mutation at location chr7:151935798-151935799 GA>TG in gene KMT2C. now what is IGV telling me exactly?

[iraun]

Well, that is not a frameshift. As far as I can see from the image you have 2 adjacent SNPs, which is sometimes termed as Multiple Nucleotide Polymorphism (MNP). The first one occurs in position 98 in which a G is mutated to T, and the second one in position 99, in which an A is mutated to G. In the small window you have the number of total reads (depth) of the given position, 333, the number of reads containing an A, C, G, T and N for the given position.

[Maryam]

Then what does DEL 7 means? because it a frameshift mutation at this position according to my data and am showing you that location with DEL 7

[iraun]

Sorry, I did not see that. Yes, there are 7 reads showing a deletion in that position. Although 45 reads say that there is a SNV there with a G.