List Variant Genotype Lite¶

This function aims to re-filter genotype file.

Command examples:¶

atav.sh --list-var-geno-lite --genotype PATH_TO_GENOTYPE_FILE --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:¶

--list-var-geno-lite: trigger list var geno lite function.

Required input option:

--genotype
--sample

--gene
--gene-boundary
--read-coverage-summary
--mann-whitney-test
--include-rvis
--effect
--polyphen
--min-exac-vqslod-snv
--min-exac-vqslod-indel
--gnomad-genome-rf-tp-probability-snv
--gnomad-genome-rf-tp-probability-indel
--gnomad-exome-rf-tp-probability-snv
--gnomad-exome-rf-tp-probability-indel
--gnomad-genome-pop
--gnomad-genome-af
--gnomad-exome-pop
--gnomad-exome-af
--exac-pop
--exac-af
--exclude-multiallelic-variant
--exclude-multiallelic-variant-2
--max-qc-fail-sample
--loo-af