how to use igv

[Karandeep Kaur]

I am new to igv. Kindly help me out. i watched a video on youtube to load vcf file on igv, but when i'm loading my vcf file that not seems same as shown in the youtube video. Why it is happen or i'm doing some mistake.

[igv-help]

Could you be more specific in your question?  Not every VCF file looks the same of course, it depends on the data contained within.   I can't make out any details on your screenshot.

[Karandeep Kaur]

i got that point. But now i want to know that in the image below (cursor at that point) There is T as well as A ( must be like reference was T and alternate is A) but in the last there is one line of SEQUENCE, there is G in the same position. What does that mean? whats the importance of that sequence line below?

[James Robinson]

I think you would benefit from reading the user guide. https://software.broadinstitute.org/software/igv/UserGuide

The last line is the reference, from your screenshot it appears that the BAM file you have loaded was aligned to a different reference than the one you have selected from the genome pulldown.   I say that because nearly every base is a mismatch.

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[Karandeep Kaur]

yes got it i selected the hg38 but i have to select hg19. Now its showing that mutation. Thank you so much.