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GEMINI set_somatic (version 0.20.1)

GEMINI database:

Only files with version 0.20.1 are accepted.

The min combined depth for tumor + normal:

default: -1 (not set) (--min-depth)

The min variant quality (VCF QUAL):

default: -1 (not set) (--min-qual)

The min somatic score (SSC):

default: -1 (not set) (--min-somatic-score)

The max frequency of the alternative allele in the normal sample:

default: -1 (not set) (--max-norm-alt-freq)

The max count of the alternative allele in the normal sample:

default: -1 (not set) (--max-norm-alt-count)

The minimum depth allowed in the normal sample to believe somatic:

default: -1 (not set) (--min-norm-depth)

The minimum frequency of the alternative allele in the tumor sample:

default: -1 (not set) (--min-tumor-alt-freq)

The minimum count of the alternative allele in the tumor sample:

default: -1 (not set) (--min-tumor-alt-count)

The minimum depth allowed in the tumor sample to believe somatic:

default: -1 (not set) (--min-tumor-depth)

A specific chromosome on which to tag somatic mutations:

e.g. chrom12 (--chrom)

What it does

Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database.