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Large-scale Analysis of Recurrent Variants in Annotations (LARVA)
OUTPUT README FILE

LARVA version 2.0
July 15, 2015

Lucas Lochovsky	and Jing Zhang
Gerstein Lab
Yale University
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This directory contains the output of LARVA for our paper "LARVA: an integrative framework for Large-scale Analysis of Recurrent Variants in noncoding Annotations" published in Nucleic Acids Research. Each class of noncoding annotations was intersected with the variants of 760 whole cancer genomes, and LARVA was used to determine significantly highly mutated annotations. Each noncoding annotation category is represented with a file in this directory that contains the -log10-transformed p-values for each annotation in that category. The columns of these files are:

(chr, start, stop, name, mutation count, gene flag, blacklist flag, length,
DNA replication timing,
-log10(BBD model p-value),
-log10(binomial model p-value),
-log10(BBD model with repl timing correction p-value),
-log10(binomial model with repl timing correction p-value),
-log10(BBD model with BH adjustment p-value),
-log10(BBD model with repl timing correction and BH adjustment p-value),
-log10(binomial model with BH adjustment p-value),
-log10(binomial model with repl timing correction and BH adjustment p-value))

The gene flag is used to indicate annotations that intersect genes and/or pseudogenes. This flag uses the following values:

0 --> no gene or pseudogene intersection
1 --> gene intersection
2 --> pseudogene intersection
3 --> both gene and pseudogene intersection

Furthermore, the blacklist flag is 1 if the annotation intersects a blacklist region, and 0 otherwise.