GenomonMutationFilter is a software package for filtering false poistive somatic mutations from cancer genome sequencing data.
Python (>= 2.7, >= 3.7), pysam packages
You can choose between realignment using blat or realignment using edlib.
git clone https://github.com/Genomon-Project/GenomonMutationFilter.git
cd GenomonMutationFilter
python setup.py build
python setup.py install
wget http://downloads.sourceforge.net/project/samtools/tabix/tabix-0.2.6.tar.bz2
tar xjvf tabix-0.2.6.tar.bz2
cd tabix-0.2.6
make
target somatic mutation candidats: the somatic mutation candidates (should be .tsv or .vcf format).
target tumor bam: the indexed bam file of the target tumor sample.
target normal bam: the indexed bam file of the target normal sample.
usage: mutfilter realignment [-h] -t TARGET_MUTATION_FILE -1 BAM1 [-2 BAM2]
[-A SAMPLE1] [-B SAMPLE2] -o OUTPUT -r REF_GENOME
[--blat] [-b BLAT_PATH] [-m tumor_min_mismatch]
[-M normal_max_mismatch] [-s score_difference]
[-w window_size] [-d max_depth]
[-F exclude_sam_flags] [-O {vcf,anno}] [--header]
[-T number_of_threads]
usage: mutfilter indel [-h] -t TARGET_MUTATION_FILE -2 BAM2 [-A SAMPLE1]
[-B SAMPLE2] -o OUTPUT [-l search_length] [-n neighbor]
[-d min_depth] [-m min_mismatch]
[-a allele_frequency_thres] [--header] -s SAMTOOLS_PATH
[-S SAMTOOLS_PARAMS] [-O {vcf,anno}] [-r REF_GENOME]
usage: mutfilter breakpoint [-h] -t TARGET_MUTATION_FILE -2 BAM2 [-A SAMPLE1]
[-B SAMPLE2] -o OUTPUT [-d max_depth]
[-c min_clip_size] [-j junc_num_thres]
[-m mapping_quality_thres] [-F exclude_sam_flags]
[--header] [-O {vcf,anno}] [-r REF_GENOME]
usage: mutfilter simplerepeat [-h] -t TARGET_MUTATION_FILE -o OUTPUT -S
SIMPLE_REPEAT_DB [--header] [-O {vcf,anno}]