From b58da139c3b07f9fe603519d530a11cc75d48a1e Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Tue, 18 Aug 2020 23:01:43 -0700 Subject: [PATCH] Clarify bwa mem -5 option Clarify that the -5 bwa mem option chooses the alignment that starts earliest in the read relative to the read/sequencing order, not genomic coordinate order --- fastmap.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fastmap.c b/fastmap.c index c865426..d2ee943 100644 --- a/fastmap.c +++ b/fastmap.c @@ -296,7 +296,7 @@ int main_mem(int argc, char *argv[]) fprintf(stderr, " -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n"); fprintf(stderr, " -o FILE sam file to output results to [stdout]\n"); fprintf(stderr, " -j treat ALT contigs as part of the primary assembly (i.e. ignore .alt file)\n"); - fprintf(stderr, " -5 for split alignment, take the alignment with the smallest coordinate as primary\n"); + fprintf(stderr, " -5 for split alignment, take the alignment with the smallest query (not genomic) coordinate as primary\n"); fprintf(stderr, " -q don't modify mapQ of supplementary alignments\n"); fprintf(stderr, " -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) []\n"); fprintf(stderr, "\n");