Service note: Geraldine is on vacation this week; other members of GSA will be responding to questions, but they have a lot of work besides this, so be aware that responses may be a little slower than usual. Thank you for your patience.
Actually, scratch that -- In this case we do want to make some adjustments by default. We'll modify the tool and document the modified behavior in the docs.
I am using UnifiedGenotyper for calling variants in a pooled sample of 3 --using sample_ploidy 6-- and was having problems calling indels. After a little bit of tinkering, it seems the problem was caused by using the default value in --minIndelFrac which by default is set to 0.25, so I set it to 0.08 Would it be a good idea to automatically lower this default value in the case of higher ploidies?
We prefer to minimize the automatic parameter adjustments, because the user should be aware of what's happening and make choices that fit their experiment. We will add a note to the docs re: pooled experiments to make users aware that this parameter should be adapted. Thanks for pointing it out!
jdavila
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I am using UnifiedGenotyper for calling variants in a pooled sample of 3 --using sample_ploidy 6-- and was having problems calling indels. After a little bit of tinkering, it seems the problem was caused by using the default value in --minIndelFrac which by default is set to 0.25, so I set it to 0.08 Would it be a good idea to automatically lower this default value in the case of higher ploidies?
Thanks,
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0 • Off Topic Disagree Agree Like WTF •We prefer to minimize the automatic parameter adjustments, because the user should be aware of what's happening and make choices that fit their experiment. We will add a note to the docs re: pooled experiments to make users aware that this parameter should be adapted. Thanks for pointing it out!
Geraldine Van der Auwera, PhD
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10 • Off Topic Disagree Agree Like WTF •