From 4a1feb505deea79d0c6e3e099f5b4d0133defdb7 Mon Sep 17 00:00:00 2001 From: Daniel E Cook Date: Mon, 10 Mar 2025 14:23:56 -0500 Subject: [PATCH] Update deepvariant-rnaseq-case-study.md --- docs/deepvariant-rnaseq-case-study.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/deepvariant-rnaseq-case-study.md b/docs/deepvariant-rnaseq-case-study.md index 4b014437..f6794a13 100644 --- a/docs/deepvariant-rnaseq-case-study.md +++ b/docs/deepvariant-rnaseq-case-study.md @@ -219,7 +219,7 @@ sudo docker run \ --output_vcf=output/HG005.output.vcf.gz \ --num_shards=$(nproc) \ --regions=data/chr20_CDS_3x.bed \ - --make_examples_extra_args="split_skip_reads=true,channel_list='BASE_CHANNELS'" \ + --make_examples_extra_args="split_skip_reads=true,channels=''" \ --intermediate_results_dir output/intermediate_results_dir ``` @@ -239,8 +239,8 @@ sudo docker run \ * `split_skip_reads=true` - *Important!* This flag is critical for RNA-seq variant calling to work properly. It enables RNA-seq data to be processed efficiently. - * `--channel_list='BASE_CHANNELS'` - Sets the channel list for the RNA-seq - model. + * `channels=''` - Resets the channel list to be appropriate for the + RNA-seq model. * `--intermediate_results_dir` - Outputs results to an intermediate directory. For running on GPU machines, or using Singularity instead of Docker, see