Question: Syntax for ContEst program to identify sample contamination
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gravatar for Genetics
3.5 years ago by
Genetics1.5k
United States
Genetics1.5k wrote:

I have been running this tool from GATK ( https://www.broadinstitute.org/cancer/cga/contest_run ) as this following command below where snps.raw.vcf is the VCF file for common SNPs,bam_156samples.list is the list of bam files (full path), sample.txt is the list of samples to be used from VCF file, and hapmap_3.3.hg19.vcf is the population data. The output (all_samples_test2_contaminated.txt) I get from this command is empty with the header line only. Can someone please tell me what is wrong with the command below?

command:

java -jar ContEst.jar -T Contamination -B:genotypes,vcf /mypath/snps.raw.vcf -BTI genotypes -B:pop,vcf /mypath/hapmap_3.3.hg19.vcf -I /mypath/bam_156samples.list -R /mypath/hg19.fasta -pc 0.1 -o all_samples_test2_contaminated.txt -sn sample.txt

all_samples_test2_contaminated.txt output file contains only the header line:

name    population  population_fit  contamination   confidence_interval_95_width    confidence_interval_95_low  confidence_interval_95_high sites
contest • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 3.5 years ago by Genetics1.5k
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