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Collapsing Lite

This function aims to re-filter genotype file to perform collapsing approach again. More details about collapsing analysis approach please check from Collapsing wiki page.

Command examples:

atav.sh --collapsing-lite --genotype PATH_TO_GENOTYPE_FILE --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--collapsing-lite: trigger collapsing 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
--exclude-false-loftee
--min-trap-score
--min-trap-score-non-coding