MutChecker is a tool for checking the mutation status of a given genome range.
mamba create -n mutchecker -c bioconda -y python==3.9 biopython==1.80 freebayes whatshap bcftools samtools htslib numexpr miniprot blast
conda activate mutchecker
pip install mutcheckerbamstat: Stat the depth and coverage of all CDS in a bam file
usage: mutchecker bamstat [-h] gff_file bam_file
Stat the depth and coverage of all CDS in a bam file
positional arguments:
gff_file reference gff file
bam_file sorted and markdup bam file
optional arguments:
-h, --help show this help message and exitreseq: Check the mutation of a specific gene by resequencing data
usage: mutchecker reseq [-h] [-i GENE_ID] [-o OUTPUT_DIR] [-e EXON_EXTEND] [-c] genome_file gff_file bam_file
Check the mutation of a specific gene by resequencing data
positional arguments:
genome_file reference genome file
gff_file reference gff file
bam_file sorted and markdup bam file
optional arguments:
-h, --help show this help message and exit
-i GENE_ID, --gene_id GENE_ID
gene id, default=None
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
output directory, default="mutchecker_output"
-e EXON_EXTEND, --exon_extend EXON_EXTEND
extend length of cds, default=500
-c, --clean clean the intermediate files, default False