From b207723ae775d28f67e6f00ffa17c96b9b68bec6 Mon Sep 17 00:00:00 2001 From: Frank Austin Nothaft Date: Sat, 1 Apr 2017 00:50:18 -0700 Subject: [PATCH] [ADAM-1465] Updating realigner CLI docs. Resolves #1465. --- docs/source/50_cli.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/source/50_cli.md b/docs/source/50_cli.md index 2a1dd81741..87dad38cc3 100644 --- a/docs/source/50_cli.md +++ b/docs/source/50_cli.md @@ -165,6 +165,15 @@ options fall into several general categories: * `-max_target_size`: The maximum length of a target to realign. Targets longer than this size are dropped before trying to realign. Defaults to 3,000bp. + * `-max_reads_per_target`: The maximum number of reads in a target that + we will try to realign. By default, this value is 20,000 reads. If we + encounter a target with more than this number of reads, we skip realigning + this target. + * `-reference`: An optional path to a reference genome assembly build. If this + is not provided, then we attempt to reconstruct the reference at each target + from the MD tags on each read. + * `-unclip_reads`: If provided, we will unclip reads when attempting to realign + them to the reference. If not provided, we leave clipped reads clipped. * `-log_odds_threshold`: The log odds threshold to use for picking a consensus sequence to finalize realignments against. A consensus will not be realigned against unless the Phred weighted edit distance against the