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
| 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 | |