Creating flow files from the command line - mjsull/HapFlow GitHub Wiki
Flow files can be created from the command-line using the following command.
$ python HapFlow.py -b <bam_file> -v <vcf_file> -o <output_prefix>
Where bam_file is and indexed bam file
vcf file is a vcf file containing called variants and
output_prefix is the prefix for all output flow files (one for each reference in BAM)
To view a created flow file from the commmand line run:
$ python HapFlow.py -l <flow_file>
optional arguments:
-h, --help show a help message and exit
-r REFERENCE, --reference REFERENCE
Only create flow file from this reference.
-r_min REF_MIN, --ref_min REF_MIN
Only use variants after this position.
-r_max REF_MAX, --ref_max REF_MAX
Only use variants before this position.
-min_q MIN_QUALITY, --min_quality MIN_QUALITY
Only use variants with a quality value greater than
this.
-max_c MAX_COVERAGE, --max_coverage MAX_COVERAGE
Only use variants with coverage less than this value *
median coverage.
-max_d MAX_DISTANCE, --max_distance MAX_DISTANCE
Maximum distance between two variants in the same
flow. (set as the upper bound of expected insert size
of reads (paired-end) or read length (single-end).
For a full description of these variables (and why you may want to alter them) see creating a flow file.