camu 0.0.6

A package for filtering candidate mutations for spontaneous mutation rate estimates.

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:

1. filterDupAndLinked.py
2. detectFIO.py
3. snapshotIGV.py