Question: Syntax for ContEst program to identify sample contamination
gravatar for MAPK
2.8 years ago by
United States
MAPK1.4k wrote:

I have been running this tool from GATK ( ) 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?


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 • 1.0k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 2.8 years ago by MAPK1.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 766 users visited in the last hour