Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
fix hyperlink referencing Discussion #64
  • Loading branch information
Faizal-Eeman authored Aug 17, 2022
1 parent 95b0ade commit 10c3331
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ The call-gSV nextflow pipeline, calls structural variants (SVs) and copy number
| `F72.config` | 72 / 136.8 GB | call_gSV_Delly; 1 / 65 GB | call_gSV_Manta; 1 / 65 GB | validate_file; 1 / 1 GB |
| `M64.config` | 64 / 950 GB | call_gSV_Delly; 1 / 470 GB | call_gSV_Manta; 1 / 470 GB | validate_file; 1 / 1 GB |
---
\* - Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set `run_manta = false` in the sample specific [config](config/template.config) file.
\* Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set `run_manta = false` in the sample specific [config](config/template.config) file.

## How To Run

Expand Down Expand Up @@ -219,7 +219,7 @@ Testing was performed leveraging aligned and sorted BAMs generated using `bwa-me
* **A-partial**: CPCG0196-B1-downsampled-a-partial-sorted.bam\*
* **SMC-HET:** HG002.N.bam

\* In Delly `v1.1.3`, a `coverage check` has been introduced which checks for coverage quality in a given window before CNV calling. Successful CNV calling was observed on samples with coverages across the genome, such as, `a-full-CPCG0196-B1.bam` and `CPCG0196-B1-downsampled-a-partial-sorted.bam` (WGS samples). For more details, please refer to Discussion #64.
\* In Delly `v1.1.3`, a `coverage check` has been introduced which checks for coverage quality in a given window before CNV calling. Successful CNV calling was observed on samples with coverages across the genome, such as, `a-full-CPCG0196-B1.bam` and `CPCG0196-B1-downsampled-a-partial-sorted.bam` (WGS samples). For more details, please refer to Discussion [#64](https://github.com/uclahs-cds/pipeline-call-gSV/discussions/64).

Test runs for the A-mini/partial/full samples were performed using the following reference files

Expand Down

0 comments on commit 10c3331

Please sign in to comment.