@@ -12,7 +12,7 @@ Text in angle brackets, e.g. `<project>` indicates variable parameters. A variab
The analysis is run with the bcbio pipeline (version 1.2.8) located at `/home/u035/u035/shared/software/bcbio`. All genome reference and annotation data resources are contained within the `genomes/Hsapiens/hg38` subfolder.
The TWIST target BED file is at: `/home/u035/u035/shared/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed`. See [resources](https://git.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome/blob/master/docs/Resources_ultra2.md).
The TWIST target BED file is at: `/home/u035/u035/shared/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed`. See [resources](Resources.md).
## Input
...
...
@@ -23,7 +23,7 @@ A 6-column tab-delimited [PED/FAM format file](https://www.cog-genomics.org/plin
### Sample id format
The sequencing reads for the samples delivered from EdGE are identified by folder name and as the 8th column in the tab-delimited text file file_list.tsv inside the dated batch folder. The identifiers are in the format:
The sequencing reads for the samples delivered from EdGE are identified by folder name and as the 8th column in the tab-delimited text file `file_list.tsv` inside the dated batch directory. The identifiers are in the format:
2. Copy the PED file for the batch to the params folder in the working area. It should be named <project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, copy it instead.
2. Copy the PED file for the batch to the params folder in the working area. It should be named `<project_id>.ped`, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, copy it instead.
