Estimate cross-sample contamination
This tool determine the percent contamination of an input bam by sample, by lane, or in aggregate across all the input reads.
These are example commands that show how to run ContEst for typical use cases. Square brackets ("[ ]") indicate optional arguments. Note that parameter values and/or resources shown here may not be the latest recommended; see the Best Practices documentation for detailed recommendations.
java
-jar GenomeAnalysisTK.jar \
-T ContEst \
-R reference.fasta \
-I tumor.bam \
--genotypes normalGenotypes.vcf \
--popFile populationAlleleFrequencies.vcf \
-L populationSites.interval_list
[-L targets.interval_list] \
-isr INTERSECTION \
-o output.txt
java
-jar GenomeAnalysisTK.jar \
-T ContEst \
-R reference.fasta \
-I:eval tumor.bam \
-I:genotype normal.bam \
--popFile populationAlleleFrequencies.vcf \
-L populationSites.interval_list
[-L targets.interval_list] \
-isr INTERSECTION \
-o output.txt
These Read Filters are automatically applied to the data by the Engine before processing by ContEst.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --popfile -pf |
NA | the variant file containing information about the population allele frequencies | |
| Optional Inputs | |||
| --genotypes |
none | the genotype information for our sample | |
| Optional Outputs | |||
| --out -o |
stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --base_report -br |
NA | Where to write a full report about the loci we processed | |
| --beta_threshold |
0.95 | threshold for p(f>=0.5) to trim | |
| --genotype_mode -gm |
HARD_THRESHOLD | which approach should we take to getting the genotypes (only in array-free mode) | |
| --lane_level_contamination -llc |
NA | set to META (default), SAMPLE or READGROUP to produce per-bam, per-sample or per-lane estimates | |
| --likelihood_file -lf |
NA | write the likelihood values to the specified location | |
| --min_mapq |
20 | threshold for minimum mapping quality score | |
| --min_qscore |
20 | threshold for minimum base quality score | |
| --minimum_base_count -mbc |
500 | what minimum number of bases do we need to see to call contamination in a lane / sample? | |
| --population |
CEU | evaluate contamination for just a single contamination population | |
| --precision -pc |
0.1 | the degree of precision to which the contamination tool should estimate (e.g. the bin size) | |
| --sample_name -sn |
unknown | The sample name; used to extract the correct genotypes from mutli-sample truth vcfs | |
| --trim_fraction |
0.01 | at most, what fraction of sites should be trimmed based on BETA_THRESHOLD | |
| Optional Flags | |||
| --verify_sample -vs |
false | should we verify that the sample name is in the genotypes file? | |
| Advanced Parameters | |||
| --fixed_epsilon_qscore |
NA | use a constant epsilon (phred scale) for calculation | |
| --min_genotype_depth |
50 | what minimum depth is required to call a site in seq genotype mode | |
| --min_genotype_llh |
5.0 | the min log likelihood for UG to call a genotype | |
| --min_genotype_ratio |
0.8 | the ratio of alt to other bases to call a site a hom non-ref variant | |
| --min_site_depth |
0 | minimum depth at a site to consider in calculation | |
| --trim_interval |
0.0 | progressively trim from 0 to TRIM_FRACTION by this interval | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Where to write a full report about the loci we processed
PrintStream NA
threshold for p(f>=0.5) to trim
double 0.95 [ [ -∞ ∞ ] ]
use a constant epsilon (phred scale) for calculation
Byte NA
which approach should we take to getting the genotypes (only in array-free mode)
The --genotype_mode argument is an enumerated type (SeqGenotypeMode), which can have one of the following values:
SeqGenotypeMode HARD_THRESHOLD
the genotype information for our sample
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
set to META (default), SAMPLE or READGROUP to produce per-bam, per-sample or per-lane estimates
Set[ContaminationRunType] NA
write the likelihood values to the specified location
PrintStream NA
what minimum depth is required to call a site in seq genotype mode
int 50 [ [ -∞ ∞ ] ]
the min log likelihood for UG to call a genotype
double 5.0 [ [ -∞ ∞ ] ]
the ratio of alt to other bases to call a site a hom non-ref variant
double 0.8 [ [ -∞ ∞ ] ]
threshold for minimum mapping quality score
int 20 [ [ -∞ ∞ ] ]
threshold for minimum base quality score
int 20 [ [ -∞ ∞ ] ]
minimum depth at a site to consider in calculation
int 0 [ [ -∞ ∞ ] ]
what minimum number of bases do we need to see to call contamination in a lane / sample?
Integer 500 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout
the variant file containing information about the population allele frequencies
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R RodBinding[VariantContext] NA
evaluate contamination for just a single contamination population
String CEU
the degree of precision to which the contamination tool should estimate (e.g. the bin size)
double 0.1 [ [ -∞ ∞ ] ]
The sample name; used to extract the correct genotypes from mutli-sample truth vcfs
String unknown
at most, what fraction of sites should be trimmed based on BETA_THRESHOLD
double 0.01 [ [ -∞ ∞ ] ]
progressively trim from 0 to TRIM_FRACTION by this interval
double 0.0 [ [ -∞ ∞ ] ]
should we verify that the sample name is in the genotypes file?
boolean false