If you're using docker
, replace mity
with:
docker run -w "$PWD" -v "$PWD":"$PWD" drmjc/mity
$ mity -h
usage: mity [-h] {call,normalise,report,merge,version} ...
Mity: a sensitive variant analysis pipeline optimised for WGS data
positional arguments:
{call,normalise,report,merge,version}
mity sub-commands (use with -h for more info)
call Call mitochondrial variants
normalise Normalise & FILTER mitochondrial variants
report Generate mity report
merge Merging mity VCF with nuclear VCF
version Display this program's version.
options:
-h, --help show this help message and exit
Usage: See the online manual for details: http://github.com/KCCG/mity
Authors: Clare Puttick, Mark Cowley
License: MIT
Version: 0.4.45
usage: mity call [-h] [-d] [--reference {hs37d5,hg19,hg38,mm10}] [--prefix PREFIX] [--min-mapping-quality MIN_MQ] [--min-base-quality MIN_BQ] [--min-alternate-fraction MIN_AF] [--min-alternate-count MIN_AC] [--p P] [--normalise]
[--output-dir OUTPUT_DIR] [--region REGION] [--bam-file-list] [-k]
files [files ...]
positional arguments:
files BAM / CRAM files to run the analysis on. If --bam-file-list is included, this argument is the file containing the list of bam/cram files.
options:
-h, --help show this help message and exit
-d, --debug Enter debug mode
--reference {hs37d5,hg19,hg38,mm10}
Reference genome version to use. Default: hs37d5
--prefix PREFIX Output files will be named with PREFIX
--min-mapping-quality MIN_MQ
Exclude alignments from analysis if they have a mapping quality less than MIN_MAPPING_QUALITY. Default: 30
--min-base-quality MIN_BQ
Exclude alleles from analysis if their supporting base quality is less than MIN_BASE_QUALITY. Default: 24
--min-alternate-fraction MIN_AF
Require at least MIN_ALTERNATE_FRACTION observations supporting an alternate allele within a single individual in the in order to evaluate the position. Default: 0.01, range = [0,1]
--min-alternate-count MIN_AC
Require at least MIN_ALTERNATE_COUNT observations supporting an alternate allele within a single individual in order to evaluate the position. Default: 4
--p P Minimum noise level. This is used to calculate QUAL score. Default: 0.002, range = [0,1]
--normalise Run mity normalise the resulting VCF
--output-dir OUTPUT_DIR
Output files will be saved in OUTPUT_DIR. Default: '.'
--region REGION Region of MT genome to call variants in. If unset will call variants in entire MT genome as specified in BAM header. Default: Entire MT genome.
--bam-file-list Treat the file as a text file of BAM files to be processed. The path to each file should be on one row per bam file.
-k, --keep Keep all intermediate files
usage: mity normalise [-h] [-d] [--output-dir OUTPUT_DIR] [--prefix PREFIX] [--allsamples] [-k] [--p P] [--reference {hs37d5,hg19,hg38,mm10}] vcf
positional arguments:
vcf vcf.gz file from running mity
options:
-h, --help show this help message and exit
-d, --debug Enter debug mode
--output-dir OUTPUT_DIR
Output files will be saved in OUTPUT_DIR. Default: '.'
--prefix PREFIX Output files will be named with PREFIX
--allsamples PASS in the filter requires all samples to pass instead of just one
-k, --keep Keep all intermediate files
--p P Minimum noise level. This is used to calculate QUAL scoreDefault: 0.002, range = [0,1]
--reference {hs37d5,hg19,hg38,mm10}
Reference genome version to use. default: hs37d5
usage: mity report [-h] [-d] [--prefix PREFIX] [--min_vaf MIN_VAF] [--output-dir OUTPUT_DIR] [-k] vcf [vcf ...]
positional arguments:
vcf mity vcf files to create a report from
options:
-h, --help show this help message and exit
-d, --debug Enter debug mode
--prefix PREFIX Output files will be named with PREFIX
--min_vaf MIN_VAF A variant must have at least this VAF to be included in the report. Default: 0.
--output-dir OUTPUT_DIR
Output files will be saved in OUTPUT_DIR. Default: '.'
-k, --keep Keep all intermediate files
usage: mity merge [-h] --mity_vcf MITY_VCF --nuclear_vcf NUCLEAR_VCF [--output-dir OUTPUT_DIR] [--prefix PREFIX] [--reference {hs37d5,hg19,hg38,mm10}] [-d] [-k]
options:
-h, --help show this help message and exit
--mity_vcf MITY_VCF mity vcf file
--nuclear_vcf NUCLEAR_VCF
nuclear vcf file
--output-dir OUTPUT_DIR
Output files will be saved in OUTPUT_DIR. Default: '.'
--prefix PREFIX Output files will be named with PREFIX. The default is to use the nuclear vcf name
--reference {hs37d5,hg19,hg38,mm10}
reference genome version to use. default: hs37d5
-d, --debug Enter debug mode
-k, --keep Keep all intermediate files