michaelfranklin/pmacutil repository overview

usage: combine_vcf.py [-h] -i I --columns COLUMNS -o O --type
                      {germline,somatic} [--regions REGIONS] [--normal NORMAL]
                      [--tumor TUMOR] [--priority PRIORITY [PRIORITY ...]]

Extracts and combines the information from germline / somatic vcfs into one

required arguments:
  -i I                  input vcfs, the priority of the vcfs will be based on
                        the order of the input. This parameter can be
                        specified more than once
  --columns COLUMNS     Columns to keep. This parameter can be specified more
                        than once
  -o O                  output vcf (unsorted)
  --type {germline,somatic}
                        must be either germline or somatic
  --regions REGIONS     Region file containing all the variants, used as
                        samtools mpileup
  --normal NORMAL       Sample id of germline vcf, or normal sample id of
                        somatic vcf
  --tumor TUMOR         tumor sample ID, required if inputs are somatic vcfs
  --priority PRIORITY [PRIORITY ...]
                        The priority of the callers, must match with the
                        callers in the source header

optional arguments:
  -h, --help            show this help message and exit

usage: add_bam_stats.py [-h] -i I -o O --type TYPE [--mpileup MPILEUP]
                        [--normal_mpileup NORMAL_MPILEUP]
                        [--tumor_mpileup TUMOR_MPILEUP]
                        [--normal_id NORMAL_ID] [--tumor_id TUMOR_ID]

Get stats from bam file and write to vcf

required arguments:
  -i I                  input vcf
  -o O                  output vcf
  --type TYPE           must be either germline or somatic
  --mpileup MPILEUP     mpileup file extracted from bam file
  --normal_mpileup NORMAL_MPILEUP
                        mpileup file extracted from the normal sample bam,
                        required if input is somatic vcf
  --tumor_mpileup TUMOR_MPILEUP
                        mpileup file extracted from the tumor sample, required
                        if input is somatic vcf
  --normal_id NORMAL_ID
                        Normal sample id, required if input is somatic vcf
  --tumor_id TUMOR_ID   Tumor sample id, required if input is somatic vcf

optional arguments:
  -h, --help            show this help message and exit