Fixed a few typos and clarified new output folder structure

docs/SOP_alignment_variant_annotation_ultra2.md

@@ -47,7 +47,7 @@ A set of paired end FASTQ files (designated by R1 or R2 suffixes), possibly more
   +---Information.txt
   +---md5_check.txt
 ```
-*Figure 1.* File name and directory structure for a batch of sequencing from Edinburgh Genomics. The EdGE project id takes the format `XXXXX\_Lastname\_Firstname`, identifying the NHS staff member who submitted the samples for sequencing. The dated batch is in the format `yyyymmdd` – in general we expect there to be only one of these per EdGE project id. The FASTQ file names relate to the sequencing run information and do not contain any information about the sample itself.
+*Figure 1.* File name and directory structure for a batch of sequencing from Edinburgh Genomics. The EdGE project id takes the format `XXXXX_Lastname_Firstname`, identifying the NHS staff member who submitted the samples for sequencing. The dated batch is in the format `yyyymmdd` – in general we expect there to be only one of these per EdGE project id. The FASTQ file names relate to the sequencing run information and do not contain any information about the sample itself.
 
 ### Reads - Edinburgh Clinical Research Facility
 
@@ -82,14 +82,14 @@ A [configuration script](../trio_whole_exome_config.sh) sets environment variabl
 
 ## Template for bcbio configuration
 
-Bcbio requires a [template file in YAML format](../trio_whole_exome_bcbio_template.yaml). to define the procedures run in the pipeline.
+Bcbio requires a [template file in YAML format](../trio_whole_exome_bcbio_template.yaml) to define the procedures run in the pipeline.
 
 ## Output
 
 Per sample: BAM file of aligned reads against the hg38 genome assembly
 Per family: Annotated VCF file and QC report
 
-Output will be in the folder `/home/u035/u035/shared/results/<version>_<project_id>` and follow the structure in *Figure 4* (with multiple instances of the indiv_id sub directories, one per sequenced family member.). The qc sub-directories are not enumerated, and automatically generated index files are not listed for brevity. An additional directory at the root of the output folder called “qc” will contain the MultiQC reports generated for an entire batch.
+Output will be in the folder `/home/u035/u035/shared/results/<short_project_id>_<version>` where `<short_project_id>` is the numeric prefix of `<project_id>` and follow the structure in *Figure 4* (with multiple instances of the indiv_id sub directories, one per sequenced family member.). The qc sub-directories are not enumerated, and automatically generated index files are not listed for brevity. An additional directory at the root of each project/version output folder called “qc” will contain the MultiQC report generated for an entire batch.
 
 ```
 <analysis_date>_<project_id>_<pcr_plate_id>_<family_id>/