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tips for checking variants in IGV

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.

igv germline bam
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updated by Vivek Vivek • written by jan jan

1 answer

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
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written by Vivek Vivek

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 ?

• 0 views • link
written by jan jan

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

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written by Vivek Vivek

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