From 76a5bab0791fe365e7b200fceb40560e8d502d85 Mon Sep 17 00:00:00 2001 From: Mark Walker Date: Fri, 25 Oct 2024 13:24:01 -0400 Subject: [PATCH] Add scramble parameters for GatherSampleEvidence doc --- .../docs/modules/gather_sample_evidence.md | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/website/docs/modules/gather_sample_evidence.md b/website/docs/modules/gather_sample_evidence.md index 4a3e8675d..ca24b6a67 100644 --- a/website/docs/modules/gather_sample_evidence.md +++ b/website/docs/modules/gather_sample_evidence.md @@ -45,6 +45,12 @@ An indexed BAM or CRAM file aligned to hg38. See [input data requirements](/docs Identifier string for the sample. Refer to the [sample ID requirements](/docs/gs/inputs#sampleids) for specifications of allowable sample IDs. IDs that do not meet these requirements may lead to errors. +#### Optional `is_dragen_3_7_8` +Default: detect automtically from BAM/CRAM header. The header check can be skippped by setting this parameter when it +is known whether the BAM/CRAM is aligned with Dragen v3.7.8. If this is true and Scramble is configured to run then +soft-clipped reads at sites called by Scramble in the original alignments will be realigned with BWA for re-calling with +Scramble. + #### Optional `collect_coverage` {#collect-coverage} Default: `true`. Collect read depth. @@ -63,6 +69,22 @@ Scramble docker image. If provided, runs the Scramble tool. #### Optional `wham_docker` {#wham-docker} Wham docker image. If provided, runs the Wham tool. +#### Optional `reference_bwa_*` +BWA-mem index files. Required only if running Scramble and the input reads are aligned to Dragen v3.7.8 + +#### Optional `scramble_alignment_score_cutoff` +Default: `60` for Dragen v3.7.8 and `90` otherwise. Minimum alignment score for consensus sequences again the MEI reference +in the Scramble tool. The default value is set automatically depending on aligner. Can be overridden to tune +sensitivity. + +#### Optional `scramble_percent_align_cutoff` +Default: `70`. Minimum alignment percent for consensus sequences again the MEI reference in the Scramble tool. Can be +overridden to tune sensitivity. + +#### Optional `scramble_min_clipped_reads_fraction` +Default: `0.22`. Minimum number of soft-clipped reads required for site cluster identification in the Scramble tool, +as a fraction of average read depth. Can be overridden to tune sensitivity. + ### Advanced parameters #### Optional `run_localize_reads`