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
Optional input option:
--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