Institut Curie - TMB analysis
This tool was designed to calculate a Tumor Mutational Burden (TMB) score from a VCF file.
The TMB is usually defined as the total number of non-synonymous mutations per coding area of a tumor genome. This metric is mainly used as a biomarker in clinical practice to determine whether to use or not immunomodulatory anticancer drugs (immune checkpoint inhibitors such as Nivolumab). Whole Exome Sequencing (WES) allows comprehensive measurement of TMB and is considered the gold standard. In practice, as TMB is mainly used in the routine of the clinic, and due to the high cost of WES, TMB calculation based on gene panels is preferred.
Currently, the main limitation of TMB calculation is the lack of standard for its calculation. Therefore, we decided to propose a very versatile tool allowing the user to define exactly which type of variants to use or filter.
The tool was implemented in python3, and require the librairies cyvcf2 and yaml.
We provide a conda file to build a simple python environment.
To do so, simply use:
conda env create -f environment.yml -p PATH_TO_INSTALL
In order to have homogenous VCF entry files and to avoid VCF ambiguities, we recommend to normalize the VCF files before calculating the TMB. This is especially useful if the VCF file contains Multi Nucleotide Variants (MNVs) or multiallelic variants.
For that we suggest to use
bcftools norm -f FASTA -m- -o file_norm.vcf file
The idea behind this script is quite simple. All variants are scanned and filtered according to the criteria provided by the user. If a variant passes all the filters, it is therefore used for the TMB calculation. In other words, if no filters are provided, the script will simply count the number of variants.
The TMB is defined as the number of variants over the size of the genomic region (in Mb). In order to calculate the size of the genome (ie. the effectiveGenomeSize), the user can provide a BED file (--bed) with the design of the assay. This BED file should be ordered, 0 based and with no header. Another alternative is to specify the size of genomic regions using --effGenomeSize. Importantly, this is the user responsability to provide the BED corresponding to the experiments.
In addition, we provide the pyEffGenomicSize.py script to calculate this genome effective size from a BED file according to a few criterias such as annotations, coverage and mapping quality thresholds defined by the user (script in bin/pyEffGenomeSize.py).
python bin/pyTMB.py -h
usage: pyTMB.py [-h] [-i VCF] [--dbConfig DBCONFIG] [--varConfig VARCONFIG]
[--sample SAMPLE] [--effGenomeSize EFFGENOMESIZE] [--bed BED]
[--vaf VAF] [--maf MAF] [--minDepth MINDEPTH]
[--minAltDepth MINALTDEPTH] [--filterLowQual] [--filterIndels]
[--filterCoding] [--filterSplice] [--filterNonCoding]
[--filterSyn] [--filterNonSyn] [--filterCancerHotspot]
[--filterPolym] [--filterRecurrence] [--polymDb POLYMDB]
[--cancerDb CANCERDB] [--verbose] [--debug] [--export]
[--version]
optional arguments:
-h, --help show this help message and exit
-i VCF, --vcf VCF Input file (.vcf, .vcf.gz, .bcf) (default: None)
--dbConfig DBCONFIG Databases config file (default:
./config/databases.yml)
--varConfig VARCONFIG
Variant calling config file (default:
./config/calling.yml)
--effGenomeSize EFFGENOMESIZE
Effective genome size (default: None)
--bed BED Capture design to use if effGenomeSize is not defined
(BED file) (default: None)
--vaf VAF Filter variants with Allelic Ratio <= vaf (default:
0.05)
--maf MAF Filter variants with MAF > maf (default: 0.001)
--minDepth MINDEPTH Filter variants with depth < minDepth (default: 5)
--minAltDepth MINALTDEPTH
Filter variants with alternative allele depth <=
minAltDepth (default: 2)
--filterLowQual Filter low quality (i.e not PASS) variant (default:
False)
--filterIndels Filter insertions/deletions (default: False)
--filterCoding Filter Coding variants (default: False)
--filterSplice Filter Splice variants (default: False)
--filterNonCoding Filter Non-coding variants (default: False)
--filterSyn Filter Synonymous variants (default: False)
--filterNonSyn Filter Non-Synonymous variants (default: False)
--filterCancerHotspot
Filter variants annotated as cancer hotspots (default:
False)
--filterPolym Filter polymorphism variants in genome databases. See
--maf (default: False)
--filterRecurrence Filter on recurrence values (default: False)
--polymDb POLYMDB Databases used for polymorphisms detection (comma
separated) (default: gnomad)
--cancerDb CANCERDB Databases used for cancer hotspot annotation (comma
separated) (default: cosmic)
--sample SAMPLE Specify the sample ID to focus on (default: None)
--debug Export original VCF with TMB_FILTER tag (default:
False)
--export Export a VCF with the considered variants (default:
False)
--verbose Active verbose mode (default: False)
--version Version numberWorking with vcf files is usually not straighforward, and mainly depends on the variant caller and annotation tools/databases used. In order to make this tool as flexible as possible, we decided to set up two configurations files to defined which fields have to be checked and in which case.
The --dbConfig file described all details about annotation. As an exemple, we provide some configurations for Annovar (config/annovar.yml)
and snpEff (config/snpeff.yaml) tool.
These files can be customized by the user.
In the same way, all parameters which are variant caller specific can be set up in another config file using the --varConfig parameter.
Config files for Varscan2 (config/varscan2.yml) and Mutect2 (config/mutect2.yml) are provided as examples.
The yaml config files must list the different keys:values for each function.
As an exemple, to assess whether a variant is coding, the programm will used (for Annovar);
isCoding:
Func.refGene:
- exonic
It will therefore search in the INFO field the key Func.refGene and the value exonic.
Regarding the databases, this is the same idea. Here is the list of databases, and fields used to check the MAF value by default (for Annovar) :
polymDb:
1k:
- 1000g2015aug_all
gnomad:
- gnomAD_exome_ALL
esp:
- esp6500siv2_all
exac:
- ExAC_ALL
The user can thus choose to scan all databases with the --polymDb 1k,gnomad,esp,exac parameter.
The same is true for the --cancerDb parameter.
Input file (.vcf, .vcf.gz, .bcf)
Specify the sample ID to focus on, useful when dealing with multisample vcfs
Specify either a sorted BED file with no header, or the size of the effective genome size to take in count.
Filter variants with Allelic Ratio < minVAF. Note the field used to get the Allelic Ratio field is defined in the config/caller.yml file. In this case, the programm will first look for this information in the FORMAT field, and then in the INFO field.
Filter variants with MAF < maf. Note the databases used to check the Min Allele Frequency are set using the --polymDb
parameters and the config/databases.yml file.
Filter variants with depth < minDepth. Note the field used to get the depth is defined in the config/caller.yml file. In this case, the programm will first look for this information in the FORMAT field, and then in the INFO field.
FIlter alternative allele with depth < minAltDepth. The programm will look in the FORMAT field exclusively.
Filter variants for which is the FILTER field is not PASS or for which the QUAL value is not null.
Filter insertions/deletions variants.
Filter Coding variants as defined in the config/databases.yml field.
Filter Splice variants as defined in the config/databases.yml field.
Filter Non-coding variants as defined in the config/databases.yml field.
Filter Synonymous variants as defined in the config/databases.yml field.
Filter Non-Synonymous variants as defined in the config/databases.yml field.
Filter variants annotated as cancer hotspots as defined in the config/databases.yml field. So far, all variants with a 'cancer' annotation (for instance with a COSMIC Id) will be removed.
Filter polymorphism variants from genome databases. The databases to considered can be listed with the --polymDb parameter.
The fields to scan for each database are defined in the config/databases.yml file and the population frequency is compared with the --minMAF field.
Filter on recurrence values (for instance, intra-run occurence). In this case, the vcf file must contains the recurrence information which can be defined the config/databases.yml file.
By default, the script outputs a few information with the calculated TMB value.
This option allows to export a vcf file which only contains the variants used for TMB calculation.
The option allows to export a vcf file with the tag TMB_FILTERS in the INFO field. This tag therefore contains the reason for which a variant would be filtered.
This tool is designed to calculate the effective genome size from a BED file. This effective size is an important parameter of TMB calculation which can have a strong impact on the results. For instance, if only coding variants are used, it would make sense to use only the genomic size of coding region for the TMB calculation. So far, this is the user responsability to provide an intial BED file with corresponding genomic features. and to specify it to the pyEffGenomeSize.py script or directly to the --bed parameter. The user can also provide the size of the BED with the --effGenomeSize parameter.
python3 pyEffGenomeSize.py -h
usage: pyEffGenomeSize.py [-h] --bed BED --gtf GTF [--bam BAM] [--mosdepth]
[--minCoverage MINCOVERAGE] [--minMapq MINMAPQ]
[--filterNonCoding] [--filterCoding]
[--featureTypes FEATURETYPES [FEATURETYPES ...]]
[--saveIntermediates] [-t THREAD]
[--oprefix OPREFIX] [--verbose] [--version]
optional arguments:
-h, --help show this help message and exit
--bed BED BED file (.bed) (default: None)
--gtf GTF GTF file for genome annotation (.gtf) (default: None)
--bam BAM BAM file for mapping statistics (.bam) (default: None)
--mosdepth enable mosdepth processing, require .bam file
(default: False)
--minCoverage MINCOVERAGE
minimum coverage of the region (default: 0)
--minMapq MINMAPQ minimum coverage of the region (default: 0)
--filterNonCoding Filter regions associated with non coding annotations
(default: False)
--filterCoding Filter regions associated with coding annotations
(default: False)
--featureTypes FEATURETYPES [FEATURETYPES ...]
List of Features (exon, gene, transcript, UTR, CDS) to
keep (3rd column from gtf/gff). Required with
--filterCoding argument (default: [])
--saveIntermediates Save mosdepth intermediate files (default: False)
-t THREAD, --thread THREAD
Number of threads for mosdepth run (default: 1)
--oprefix OPREFIX Suffix for filtered bed (default: pyeffg)
--verbose Active verbose mode (default: False)
--version Version numberThe input BED from to filter. This file should be 0 based, sorted and with no header
A sorted gtf file to extract annotations from, for example gencode.v19.annotation.gtf
A bam file from your experiment to extract mapping quality and coverage information
To run mosdepth and extract regions with specific coverage and mapping quality. This is an optionnal parameters, but if used, it requires --bam parameter.
Define the minimum coverage accepted for each region of the BED file
Mapping quality threshold. reads with a mapping quality less than this are ignored
This filter removes regions considered as non coding from the gtf and BED files to only keep exonic regions.
This filter removes regions considered as coding based on the transcript_type field in the gtf.
This filter requires the parameter featureTypes
This parameter offers the possibility to choose one or multiple features to select from the following ("exon", "gene", "transcript", "UTR", "CDS") to keep in the final BED file.
Here is a list of recommended parameters for different user cases.
Let's calculated the TMB on a gene panel vcf file (coding size = 1.59Mb, caller = varscan, annotation = Annovar) with the following criteria:
- minDepth at 100X
- non-synonymous
- coding and splice
- non polymorphism variants using 1K, gnomAD databases and a MAF of 0.001
In this case, a typical usage would be :
python pyTMB.py -i ${VCF} --effGenomeSize 1590000 \
--dbConfig config/annovar.yml \
--varConfig config/varscan.yml \
--minMAF 0.001 --minDepth 100 --minAltDepth 2\
--filterLowQual \
--filterNonCoding \
--filterSplice \
--filterSyn \
--filterPolym --polymDb 1k,gnomad \
--export > TMB_results.log
For WES, we recommend filtering low quality, non coding, synonymous, polymorphic variants. Here, indels and splicing variants are kept. For WES, an effective Genome size of 33Mb is used but a tailored size depending on the variants and regions is preferred.
In the case of a WES variant calling using Mutect2 as variant caller and Snpeff as annotation tool, a typical usage would be :
python pyTMB.py -i ${VCF} --effGenomeSize 33280000 \
--dbConfig config/snpeff.yml \
--varConfig config/mutect2.yml \
--vaf 0.05 --maf 0.001 --minDepth 20 --minAltDepth 2 \
--filterLowQual \
--filterNonCoding \
--filterSyn \
--filterPolym --polymDb 1k,gnomad > TMB_results.log
This pipeline has been written by the bioinformatics core facility in close collaboration with the Clinical Bioinformatics and the Genetics Service of the Institut Curie. Many thanks to the seqOIA-IT team for their help in the development and for the extensive testing of the tool !
For any question, bug or suggestion, please use the issues system or contact the bioinformatics core facility.