Comments (3)
Hello, LoFreq doesn't filter by allele frequency unless you specifically request it. If you have sufficient and/or high quality variant bases at a certain position their variant quality will be high and you should see that variant.
Andreas
from lofreq.
I wonder what the smallest variation frequency LoFreq can detect ? Because I have a sample with 8 sites of 1% allele frequence. When I tested this software, I did not find all of them. Did you have any test? Or is there any parameter can I set to get more variants. Thank you!
from lofreq.
Hello, sorry, I have no idea why this has been without a reply for so long. My apologies. Regarding your question: In the original paper we wetlab-validated variants at 0.5% (and that's when validation gets tricky). There is no theoretical limit as LoFreq's resolution depends on coverage and qualities only. It's likely that your "missed" variants are simply filtered, for example by the strand bias which is applied by default. You can switch default filtering off with the --no-default-filter
option in lofreq call
. Andreas
from lofreq.
Related Issues (20)
- No sample column
- Variants missing in parallel mode HOT 2
- lofreq p-value
- Warning: Didn't find any variants in input HOT 2
- Lofreq call-parallel applies filters with --no-default-filter option specified HOT 2
- lofreq call-parallel will hang forever on subprocess error
- Filter depend on number of cores?
- cpus count versus available cpus
- Problem of forget to indel alignment-quality to your bam-file HOT 4
- Permant error in the first step HOT 1
- lofreq vcfplot issues HOT 2
- how to call multiple-sample variants HOT 4
- subprocess.CalledProcessError: non-zero exit status 1
- HTSLIB Variable HOT 2
- subprocess.CalledProcessError: non-zero exit status 1 HOT 4
- IndexError: list index out of range HOT 7
- MGI T7 or T10 data
- What are the stringent outputs and why do I have different calling results?
- Lofreq vcfplot - python version 3 support
- Lofreq viterbi
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