From 2bd443f885f2d1899126b2c60c28c485a56cbcd5 Mon Sep 17 00:00:00 2001 From: Jacob Morrison Date: Mon, 7 Oct 2024 10:37:23 -0400 Subject: [PATCH] Update vcf2bed min covg to 1 This change in defaults is to better match other tools, while also serving as a better default with the increase of scWGBS protocols. --- src/vcf2bed.c | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/vcf2bed.c b/src/vcf2bed.c index 02badb8..18ae78b 100644 --- a/src/vcf2bed.c +++ b/src/vcf2bed.c @@ -302,7 +302,7 @@ static int usage(conf_t *conf) { fprintf(stderr, "\n"); fprintf(stderr, "Options:\n"); fprintf(stderr, " -t STR Extract type {c, cg, ch, hcg, gch, snp} [%s]\n", conf->target); - fprintf(stderr, " -k INT Minimum coverage [%d]\n", conf->mincov); + fprintf(stderr, " -k INT Minimum coverage (see Note 1) [%d]\n", conf->mincov); fprintf(stderr, " -s STR Sample, (takes \"FIRST\", \"LAST\", \"ALL\", or specific\n"); fprintf(stderr, " sample names separated by \",\") [FIRST]\n"); fprintf(stderr, " -e Show context (reference base, context group {CG,CHG,CHH},\n"); @@ -311,12 +311,16 @@ static int usage(conf_t *conf) { fprintf(stderr, " -c Output Beta-M-U instead of Beta-Cov.\n"); fprintf(stderr, " -h This help\n"); fprintf(stderr, "\n"); + fprintf(stderr, "Note 1: Starting with version 1.6.0, the default minimum coverage was changed from\n"); + fprintf(stderr, " three (3) to one (1) to better match other tools and serve as a better default\n"); + fprintf(stderr, " for single-cell experiments.\n"); + fprintf(stderr, "\n"); return 1; } int main_vcf2bed(int argc, char *argv[]) { - conf_t conf = {.mincov=3, .showctxt=0, .showmu=0}; + conf_t conf = {.mincov=1, .showctxt=0, .showmu=0}; strcpy(conf.target, "CG"); char *target_samples = NULL;