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, 09:59, 15 April 2019
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| = Introduction = | | = Introduction = |
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− | '''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. |
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| = Download = | | = Download = |
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| '''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/] | | '''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/] |
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− | '''Ubuntu 16.04 x64 Binary''' [[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]] |
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| + | = Installation = |
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| + | The easiest way to install VICES is to use cget as follows: |
| + | cget install --prefix <install_prefix> gjmzajac/VICES |
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| + | 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. |
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| = Usage = | | = Usage = |
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| = VICES Example = | | = VICES Example = |
− | Coming soon
| + | '''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 |
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| + | '''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 |
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| = Citation = | | = Citation = |