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= Introduction =
= Introduction =
'''VICES''' is a program that jointly estimates the proportion of contaminating DNA in samples genotyped on arrays and which other samples in the study it came from.
'''VICES''' is a program that jointly estimates the proportion of contaminating DNA in samples genotyped on arrays and which other samples in the study the contaminating DNA came from.
= Download =
= Download =
'''Ubuntu 16.04 x64 Binary''' [[File:vices_v1.0.tar.gz|vices_v1.0.tar.gz]]
'''Ubuntu 16.04 x64 Binary''' [[File:vices_v1.0.tar.gz|vices_v1.0.tar.gz]]
= Installation =
The easiest way to install VICES is to use cget as follows:
cget install --prefix <install_prefix> gjmzajac/VICES
Alternatively, you can setup a dev environment cmake directly.
cd vices
cget install -f ./requirements.txt # Install dependencies locally.
mkdir build && cd build # Create out of source build directory.
cmake -DCMAKE_TOOLCHAIN_FILE=./cget/cget/cget.cmake .. # Configure project with dependency paths.
make # Build.
= Usage =
= Usage =
= VICES Example =
= VICES Example =
'''Download Sample Files''' [[File:vices_test.zip|vices_test.zip]]
'''Basic Command''' from within the directory with the example files:
~/vices/build/vices -r vices.test.report.list.txt -s vices.test.report.iids.txt -o vices.test.report.contam.txt
'''Expected Output''' in vices.test.report.contam.txt:
Recipient_ID Estimated_contamination Sources
iid_01 0.0107758 AF:0.00351165; Donor_iid_02:0.00726419
iid_02 0.0371312 Donor_iid_01:0.0187088; Donor_iid_03:0.0184223
iid_03 0.0791742 Donor_iid_01:0.0236221; Donor_iid_02:0.0165325; Donor_iid_08:0.0390197
iid_04 0.0158945 AF:0.0158945
iid_05 0.0535897 AF:0.025121; Donor_iid_04:0.0284687
iid_06 0.0740575 AF:0.0346833; Donor_iid_04:0.0117261; Donor_iid_10:0.0276482
iid_07 0.00551559 AF:0.00551559
iid_08 -0.00673222 AF:-0.00673222
iid_09 0.000255342 AF:0.000255342
iid_10 9.90153e-05 AF:9.90153e-05
iid_11 -0.00138426 AF:-0.00138426
iid_12 -0.00588946 AF:-0.00588946
= Citation =
= Citation =
