cmgantwerpen/pangolin repository overview

docker pull cmgantwerpen/pangolin:1.0.1

docker run --gpus all -v /data:/data cmgantwerpen/pangolin:1.0.1 \
       pangolin \
       --variant_batchsize 1024 \
       --tensor_batchsize 256 \
       /data/variants.in.vcf \
       /data/hg38.fasta \
       /data/gencode.db \
       /data/variants.out

usage: pangolin [-h] [-c COLUMN_IDS] [-m {False,True}] [-s SCORE_CUTOFF] [-d DISTANCE] [--score_exons {False,True}] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--tmpdir TMPDIR] [--variant_batchsize VARIANT_BATCHSIZE]
                [--tensor_batchsize TENSOR_BATCHSIZE]
                variant_file reference_file annotation_file output_file

positional arguments:
  variant_file          VCF or CSV file with a header (see COLUMN_IDS option).
  reference_file        FASTA file containing a reference genome sequence.
  annotation_file       gffutils database file. Can be generated using create_db.py.
  output_file           Prefix for output file. Will be a VCF/CSV if variant_file is VCF/CSV.

options:
  -h, --help            show this help message and exit
  -c COLUMN_IDS, --column_ids COLUMN_IDS
                        (If variant_file is a CSV) Column IDs for: chromosome, variant position, reference bases, and alternative bases. Separate IDs by commas. (Default: CHROM,POS,REF,ALT)
  -m {False,True}, --mask {False,True}
                        If True, splice gains (increases in score) at annotated splice sites and splice losses (decreases in score) at unannotated splice sites will be set to 0. (Default: True)
  -s SCORE_CUTOFF, --score_cutoff SCORE_CUTOFF
                        Output all sites with absolute predicted change in score >= cutoff, instead of only the maximum loss/gain sites.
  -d DISTANCE, --distance DISTANCE
                        Number of bases on either side of the variant for which splice scores should be calculated. (Default: 50)
  --score_exons {False,True}
                        Output changes in score for both splice sites of annotated exons, as long as one splice site is within the considered range (specified by -d). Output will be: gene|site1_pos:score|site2_pos:score|...
  --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set the logging level. (Default: INFO)
  --tmpdir TMPDIR       Location to create temporary directory for storing intermediate files.
  --variant_batchsize VARIANT_BATCHSIZE
                        Number of variants to score in a single CPU batch. (Default: 1280)
  --tensor_batchsize TENSOR_BATCHSIZE
                        Number of variants to process in a single GPU batch. (Default: 128)