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Old 04-08-2010, 07:19 AM   #1
Francesco Lescai
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Default SNP calling - is there an accepted Phred quality threshold?

I just would like to know if there is an established Phred quality threshold in the literature in order to consider a SNP call reliable.
Provided the depth is higher than 30x (as showed in many papers), is the Phred Quality threshold to be chosen related to the coverage?
Are there commonly accepted criteria?

Last edited by Francesco Lescai; 04-08-2010 at 07:23 AM.
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Old 04-09-2010, 08:30 PM   #2
apratap
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Hi

I am also looking at the thresholds that I could use to filter the SNP calls. I have seen people using SNP quality cut off at 50 but not in some paper that I could refer you to.

If anyone can educate me on what good thresholds could be it would help.

The parameters in question are :

1. SNP Quality
2. Depth
3. Avg Base quality of all bases taking part in the SNP call.

Thanks!
-Abhi
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Old 04-09-2010, 10:46 PM   #3
nilshomer
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Quote:
Originally Posted by apratap View Post
Hi

I am also looking at the thresholds that I could use to filter the SNP calls. I have seen people using SNP quality cut off at 50 but not in some paper that I could refer you to.

If anyone can educate me on what good thresholds could be it would help.

The parameters in question are :

1. SNP Quality
2. Depth
3. Avg Base quality of all bases taking part in the SNP call.

Thanks!
-Abhi
Given you have sufficient coverage, making you sure you see the variant allele on both strands at least once is a great filter.
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Old 04-13-2010, 11:51 AM   #4
bioinfosm
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I have seen filtering out adjoining SNP calls is also useful. Many false positives are positions next to each other on reference.
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