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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Homozygous STRs #123

Open depreeuwj opened 3 years ago

depreeuwj commented 3 years ago

Hi,

This tool is really great, thank you very much for creating it and making it very easy to use! I was wondering if there is a quality (filter) criteria if a homozygous STR is present. Is there a minimum coverage of spanning reads to receive a PASS for these cases?

Many thanks!

egor-dolzhenko commented 3 years ago

Thanks for the question! There is no explicit cutoff on the number of spanning reads at the moment. We will work on adding something like a genotype quality score to help with filtering weak calls.

Meanwhile, REViewer could be used to visually assess calls of interest.

depreeuwj commented 3 years ago

Thanks! I have a patient with the following results (Expansion Hunter version v3.2.2) :

STR | FILTER | SO | REPCI | ADSP STR1 | LowDepth | SPANNING/SPANNING | 10-10/10-10 | 4/4 STR2 | PASS | SPANNING/SPANNING | 4-4/7-7 | 4/3 STR3 | PASS | SPANNING/SPANNING | 3-3/3-3 | 10/10

So based on this, I would say that homozygous STRs below an allelic depth of 10 are flagged as "lowDepth", is this correct?

egor-dolzhenko commented 3 years ago

The LowDepth filter is set when either (a) the overall coverage of the repeat region is below 10x or (b) the number of reads crossing the boundary between the left (or the right) flank and the repeat is fewer than 5. Note that both spanning and flanking reads are used to calculate (b). Also, the same filter applies to both homozygous and heterozygous STRs.

Apologies if I did not explain this well. Would it be useful to make a diagram showing how the filer works?

depreeuwj commented 3 years ago

Hi Egor, no problem, this is already very helpfull. I think I can further continue without a diagram, thank you very much!

egor-dolzhenko commented 3 years ago

Happy to help! Please let me know if you have any other questions.