A package for filtering candidate mutations for spontaneous mutation rate estimates.
Project description
Filtering false-positive candidate mutations to accelerate DNM-counting for direct µ estimates
For direct estimation of the spontaneous mutation rate µ, it is necessary to calculate the rate of spontaneous de-novo mutations (DNM) occuring per site per generation. Consequently, counting DNM is essential for estimating µ.
The raw approach is:
- Sequencing samples and control --> .fastq files
- Assembly of sequencing results --> .bam files
- perform some filtering steps
- Variant calling
- extraction of variants occurring in samples but not in control --> candidate mutations
The resulting list of candidate mutations (CM) currently has to be manually curated using a genome browser like IGV.
Unfortunately, approx. 90 % of these CM are no true DNM, they turn out to be false-positives.
Camufi.py aims to accelerate the whole procedure of DNM counting by filtering out the vast majority of false-positive CM and by preparing the remaining CM for fast manual curation with IGV.
Camufi.py consists of 3 main Python modules:
filterDupAndLinked.py
detectFIO.py
snapshotIGV.py
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