Changes

  ./vices -r reports_list.txt -o contam_estimates.txt

  ./vices -r reports_list.txt -o contam_estimates.txt

The file must list the paths of all the Illumina report files (either plaintext or gzipped, for example see https://support.illumina.com/downloads/humanomniexpress-12-v1-1-product-support-files.html) you are testing. Output is only by stdout at this stage so you will have to redirect. All files in a single run must be from the same type and version of array with exactly the same markers.

The output consists of a header (with the number of samples, markers, etc.) then three tab-delimited columns:

*'''Recipient_Index''' the index (starting with 0) of the samples being tested. These are in the same order as in the file with paths to report files provided to VICES. If the --sample-list option is used and points to a file containing sample IDs in the same order as the report files, then this column becomes '''Recipient_ID'''.

*'''Sources''' A breakdown of the estimated sources of contamination. Most will have only one source (AF for allele frequencies) because VICES does not perform the donor search for samples with estimated contamination proportion < 0.005 by AF.

Example (simulated) report files and output are provided in the section below

We highly recommend running VICES only within the same batches they were genotyped in as the donor estimation can take a long time if you give it a long list of over 1000 samples. Other reasons to run in batches are that samples genotyped in different runs are probably less likely to have traded DNA, and batch effects may influence the calculation of allele frequencies, an important initial step in VICES. Your sequencing core should provide some information on batches. If you don't have any batch information, then running VICES on one (or at most 20) 96-well plate at a time should also work well.  

I highly recommend running VICES only within the same batches they were genotyped in as the donor estimation can take a long time if you give it a long list of over 1000 samples. Other reasons to run in batches are that samples genotyped in different runs are probably less likely to have traded DNA, and batch effects may influence the calculation of allele frequencies, an important initial step in VICES. Your sequencing core should provide some information on batches. If you don't have any batch information, then running VICES on one (or at most 20) 96-well plate at a time should also work well.  

If any duplicate/twin samples are contaminated, this could bias the results. You might want to consider excluding one of each duplicate/twin pair before running/rerunning.

If any duplicate/twin samples are contaminated, this could bias the results. You might want to consider excluding one of each duplicate/twin pair before running/rerunning.

To answer some questions I have received, no external allele frequencies are required. VICES calculates these directly from the report files you provide. If there is sufficient interest, providing external frequencies may become an option in the official release.  

No external allele frequencies are required. VICES calculates these directly from the report files you provide.

= Options =

= Options =

  -h, --help                            This help page

  -h, --help                            This help page

= VICES Example =

= Example Data =

 

= Citation =

= Citation =

A paper is in the works and should be published soon. For now, you can cite our abstract from the 2017 Biology of Genomes meeting

A paper is in the works and should be published soon. For now, you can cite our abstract from the 2017 Biology of Genomes meeting