Hi,
I would like to know what 'Source quality' means, and how the -s and -S options affect its computation. I'm trying to call human variants, including indels. As suggested in the online documentation, I would like to use dbSNP, however NCBI holds several databases and I'm not sure which one to use. I hope that understanding what 'source quality' means, will help me decide what is the most suitable database for my current problem.
Thank you,
Eugenia
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thanks for you patience, while waiting for a reply. Source quality was a
rather experimental attempt to add one more error source to LoFreq's core:
it tries to account for contamination/mismappings etc. by looking at the
amount of mismatches in a read (think of it as a variation of mapping
quality). An accumulation of mismatches in a particular read leads to a
penalty. However, you will want to ignore known variants, during the
mismatch counting and for this you can for example use dbSNP. Any
equivalent with an extensive list of known variants (including false
positives) will do actually. Having said all this, LoFreq should work just
fine without source quality...
Hi,
I would like to know what 'Source quality' means, and how the -s and -S
options affect its computation. I'm trying to call human variants,
including indels. As suggested in the online documentation, I would like to
use dbSNP, however NCBI holds several databases and I'm not sure which one
to use. I hope that understanding what 'source quality' means, will help me
decide what is the most suitable database for my current problem.
Hi,
I would like to know what 'Source quality' means, and how the -s and -S options affect its computation. I'm trying to call human variants, including indels. As suggested in the online documentation, I would like to use dbSNP, however NCBI holds several databases and I'm not sure which one to use. I hope that understanding what 'source quality' means, will help me decide what is the most suitable database for my current problem.
Thank you,
Eugenia
Dear Eugenia,
thanks for you patience, while waiting for a reply.
Source qualitywas arather experimental attempt to add one more error source to LoFreq's core:
it tries to account for contamination/mismappings etc. by looking at the
amount of mismatches in a read (think of it as a variation of mapping
quality). An accumulation of mismatches in a particular read leads to a
penalty. However, you will want to ignore known variants, during the
mismatch counting and for this you can for example use dbSNP. Any
equivalent with an extensive list of known variants (including false
positives) will do actually. Having said all this, LoFreq should work just
fine without source quality...
Hope this helps,
Andreas
Andreas
On Wed, 15 Aug 2018 at 02:18, Eugenia Zarza zarzamora23@users.sourceforge.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC