tips for checking variants in IGV

Question

[jan]

Hi,

I need to check some germline variants on IGV from BAM files based on their positions.

Is there a good tutorial/guide on how to set up parameters/filters in IGV and the reasoning behind them?

Im only aware of the basic parameters such as strand-bias, variant on >20% reads.

Answer 1

[Vivek]

Some things I look at:

1. Base qualities at the locus and mapping qualities of the reads supporting the variant
2. Frequency of mutations or INDELs within 1 KB region on either side
3. Allele fraction on both strands

[jan]

Thank you for your feedback. Apart from that, I would also like to know what kind of parameters should I set ?

For example in View > Alignments ; there are few options such as Alignment Track Options (particularly mapping quality threshold), Coverage Track options, etc?

Is it ok if I just leave everything at default setting ?

[Vivek]

Defaults should be fine, I never experimented with those. You'll be doing manual inspection anyways.