From 12ca380131d95c7831735a9fa94505a2f1b2761a Mon Sep 17 00:00:00 2001 From: Lydia Andreyevna Krasilnikova Date: Wed, 22 Nov 2023 17:44:19 -0500 Subject: [PATCH] added user option to specify masked positions --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 4b4f395..1ad99b9 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,7 @@ OPTIONS: -1 | --read-depths FILE(S) Read depth tables; provide alongside vcf files or heterozygosity tables if min-depth>0; see documentation for format [null] -g | --min-covered FLOAT Minimum proportion genome that must be covered at minimum read depth for a sample to be included [0.95] -y | --max-mismatches INT In flagged potential cross-contamination, maximum allowed unambiguous bases in contaminating sample consensus not matching contaminated sample alleles [1] + -3 | --masked-positions STRING 1-indexed positions to mask (e.g., 1-10,50,55-70) [null] - Plate map and neighbors (any combination, all optional): -m | --plate-map FILE(S) Optional plate map(s) (tab-separated, no header: sample name, plate position (e.g., A8)); provides substantial speed-up [null] @@ -335,6 +336,9 @@ By default, ≥95% of the genome must be unambigously covered for a sample to be `--min-depth` `--read-depths` +`--masked-positions` + +Use `--masked-positions` to specify positions that should be masked, for example positions known to have high rates of sequencing error. Masked positions are not included as input consensus or minor alleles. Use `--min-depth` to set the minimum number of reads that must overlap a position in a sample in order for that position to be included. If a position does not pass the read depth filter, it is not included in the numerator of [genome coverage](#sample-inclusion-thresholds) and is not included as a heterozygous position.