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 |