pip install -r requirements.txt

python setup.py install

usage: primerdesign [-h] (-l LOVD | --region REGION) [-p PADDING]
                    (-x XML | -t TSV) -b BAM [-s SAMPLE]
                    [--min-margin MIN_MARGIN] [--strict] [--m13]
                    [--m13-forward M13_FORWARD] [--m13-reverse M13_REVERSE]
                    [-f FIELD] [-af ALLELE_FREQ] [-fq1 FQ1] [-fq2 FQ2] -R
                    REFERENCE [--dbsnp DBSNP] --primer3 PRIMER3 [--bwa BWA]
                    [--samtools SAMTOOLS] [--settings-json SETTINGS_JSON]
                    [--thermodynamic-params THERMODYNAMIC_PARAMS]
                    [--ignore-errors]

optional arguments:
  -h, --help            show this help message and exit
  -l LOVD, --lovd LOVD  Input LOVD file
  --region REGION       Input region file
  -p PADDING, --padding PADDING
                        Padding around regions or variants in bases. Defaults
                        to 100
  -x XML, --xml XML     Output Miracle XML file
  -t TSV, --tsv TSV     Output TSV file
  -b BAM, --bam BAM     Path to output BAM file containing primers
  -s SAMPLE, --sample SAMPLE
                        Same ID for regions
  --min-margin MIN_MARGIN
                        Minimum distance from region or variant. Default = 10
  --strict              Enable strict mode. Primers with products larger than
                        max product size will NOT be returned
  --m13                 Output primers with m13 tails
  --m13-forward M13_FORWARD
                        Sequence of forward m13 tail
  --m13-reverse M13_REVERSE
                        Sequence of reverse m13 tail
  -f FIELD, --field FIELD
                        Name of field in DBSNP file for allele frequency
  -af ALLELE_FREQ, --allele-freq ALLELE_FREQ
                        Max accepted allele freq
  -fq1 FQ1              Path to forward fastq file for primer output. Set if
                        you want to export your primers in fastq format
                        (qualities will be sanger-encoded 40)
  -fq2 FQ2              Path to reverse fastq file for primer output. Set if
                        you want to export your primers in fastq format
                        (qualities will be sanger-encoded 40)
  -R REFERENCE, --reference REFERENCE
                        Path to reference fasta file
  --dbsnp DBSNP         Path to DBSNP vcf
  --primer3 PRIMER3     Path to primer3_core exe
  --bwa BWA             Path to BWA exe
  --samtools SAMTOOLS   Path to samtools exe
  --settings-json SETTINGS_JSON
                        Optional path to primer3 settings json file.
  --thermodynamic-params THERMODYNAMIC_PARAMS
                        Optional path to primer3 thermodynamic parameters
                        location
  --ignore-errors       Ignore errors