Deprecated and merged into https://github.com/bcgsc/WGS_TMB
This container will run the following tools in order to estimate the TMB for the provided sample: Manta V1.6.0 Strelka 2.9.2 SnpEff 4.3t GRCh37.75 msisensor 0.2
The steps of analysis are:
- If necessary, count the non-N bases of the provided reference on the 1-22,X,Y chromosomes
- Call SVs with Manta (recommended for Strelka 2)
- Call SNVs and Indels with Strelka 2
- Annotate with snpEff
- Calculate MSI with msisensor
This container is designed to be run using Singularity. Testing was performed using Singularity Version 3.0.1-104.g4feafc42.dirty.el7.
To download the container:
singularity pull library://richardcorbett/profyle_tmb/profyle_tmb:*version*
for example:
singularity pull library://richardcorbett/profyle_tmb/profyle_tmb:v0_0_2
To run you must provide the absolute paths to files that are required. This can be done by using the --bind parameters to singularity like this:
singularity run --bind /path/to/reference/fasta:/ref,/path/to/tumour_bam/folder/:/tumour_path,/path/to/normal_bam/folder/:/normal_path profyle_tmb_v0_0_1.sif -t /tumour_path/tumour_bam.bam -n /normal_path/normal.bam -r /ref/hg19a.fa -o `pwd`
- All steps will use 48 threads where possible
- The machine where analysis is performed should have at least 64Gb of RAM
- Due to the nature of the analysis applying the container to many samples (>20) at once may add heavy load to your filesystem.
- The raw VCF files for each type of analysis are compressed and kept. This may result in up to 500Mb of files for each sample.
The output folder will contain a file named results.txt where the following will be reported:
| Field | Comment |
|---|---|
| Non-N bases in 1-22,X,Y | Count of the bases used as the whole genome calculation denominator |
| CDS bases in 1-22,X,Y | Count of the unique CDS bases used in the coding calculation denominator |
| Total genome SNVs | Number of passed SNVs called by Strelka 2 |
| xTotal genome Indels | Number of passed Indels called by Strelka 2 |
| Coding SNVs | Number of passed Coding SNVs called by Strelka 2 |
| Coding Indels | Number of passed Coding Indels called by Strelka 2 |
| Genome SNV TMB | total_SNVs * 1000000 / total_bases |
| Genome Indel TMB | total_Indels * 1000000 / total_bases |
| Coding SNV TMB | coding_SNVs * 1000000 / CDS_bases |
| Coding Indel TMB | coding_Indels * 1000000 / CDS_bases |
| MSI score | Fraction of sites reported as MSI by MSIsensor |