Germline Targeted Seq. MEI Calling
Implementation of the targeted_seq_mei_calling
step
The targeted_seq_mei_calling
step takes as the input the results of the ngs_mapping
step
(aligned reads in BAM format) and performs germline mobile element insertion (MEI) identification.
The result are VCF files with mobile insertions.
Stability
This step is considered experimental, use it at your own discretion.
Step Input
MEI identification step uses Snakemake sub workflows for using the
result of the ngs_mapping
step.
Step Output
For all samples, MEI identification will be performed on the primary DNA NGS libraries separately for each configured read mapper and mobile element identification tool. The name of the primary DNA NGS library will be used as an identification token in the output file.
For each read mapper, MEI tool, and sample the following files will be generated:
{mapper}.{mei_tool}.{lib_name}.vcf.gz
{mapper}.{mei_tool}.{lib_name}.vcf.gz.md5
For example, it might look as follows for the example from above:
output/
+-- bwa.scramble.P001-N1-DNA1-WES1
| `-- out
| |-- bwa.scramble.P001-N1-DNA1-WES1.vcf.gz
| |-- bwa.scramble.P001-N1-DNA1-WES1.vcf.gz.md5
[...]
Global Configuration
Not applicable.
Default Configuration
The default configuration is as follows.
step_config:
targeted_seq_mei_calling:
#path_ngs_mapping: ../ngs_mapping
#tools: # Options: 'scramble'
# - scramble
#scramble:
#
# # path to FASTA reference with BLAST DB (`makeblastdb`)
# blast_ref: # REQUIRED
#
# # MEI reference file (FASTA), if none provided will use default.
# mei_refs:
#
# # minimum cluster size, depth of soft-clipped reads.
# n_cluster: 5
#
# # minimum MEI alignment score.
# mei_score: 50
#
# # minimum INDEL alignment score.
# indel_score: 80
#
# # minimum fraction of clipped length for calling polyA tail.
# mei_polya_frac: 0.75
Available MEI Identification Tools
The following germline MEI identification tool is currently available:
"Scramble"
Reports
Not applicable.
Parallel Execution
Not available.