From ee494e0f139488f210cb9cc8c23d35bdc71bf799 Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Mon, 19 Jun 2023 11:05:19 -0700 Subject: [PATCH] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 472dd8f..7007910 100644 --- a/README.md +++ b/README.md @@ -144,7 +144,6 @@ Other arguments - `--add_chr_tag`: If you have a mix of hg19 and GRCh37 amplicons, you can set `--ref hg19` and `--add_chr_tag` to classify them all together. - `--min_flow`: Minumum cycle CN flow to consider among decomposed paths (default=1). - `--min_size`: Minimum cycle size (in bp) to consider as valid amplicon (default=5000). -- `--report_comlexity`: Report a measurement of the amplicon's 'complexity' score, which represents a measurement of the complexity of the AA breakpoint graph decomposition. - `--verbose_classification`: Output verbose information in the `amplicon_classification_profiles.tsv` file, and create `edge_classification_profiles.tsv`. Useful for debugging. - `--force`: Disable No amp/Invalid class, if possible. Use only when extremely large CN seeds were used in AA amplicon generation (>10 Mbp intervals). - `--plotstyle [noplot, individual]`: Produce a radar-style plot of classification strengths. Default `noplot`. @@ -152,7 +151,7 @@ Other arguments - `--exclude_bed`: Provide a bed file of regions to ignore during classification. Useful for separating linked amplicons or augmenting low-complexity annotations. - `--no_LC_filter`: Set this to turn off filtering low-complexity & poor mappability genome region paths & cycles. - `--no_LC_filter`: Set this to turn off filtering low-complexity & poor mappability genome region paths & cycles. -- `"--filter_similar`: Only use if all samples are of independent origins (not replicates and not multi-region biopsies). Permits filtering of false-positive amps arising in multiple independent samples based on similarity calculation. +- `--filter_similar`: Only use if all samples are of independent origins (not replicates and not multi-region biopsies). Permits filtering of false-positive amps arising in multiple independent samples based on similarity calculation. ### 5. Other utilities: