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
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][1] 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][2]. 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.


  [1]: https://www.genome.gov/genetics-glossary/Frameshift-Mutation
  [2]: https://en.wikipedia.org/wiki/Variant_Call_Format