Deprecated and merged into https://github.com/bcgsc/WGS_TMB

PROFYLE_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:

1. If necessary, count the non-N bases of the provided reference on the 1-22,X,Y chromosomes
2. Call SVs with Manta (recommended for Strelka 2)
3. Call SNVs and Indels with Strelka 2
4. Annotate with snpEff
5. Calculate MSI with msisensor

Getting started

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`

Please Note

• 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.

Output

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