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Swedish schizophrenia controls

**Note: In working on getting together an artifact list, we realized that the vcfs for these samples are restricted to custom capture regions (whose boundaries are not specified), while the coverage data is not restricted. This means that if you use these samples, you will get hom ref calls for them that should not actually be hom ref. While most of the ccds should be ok because most of it will be part of the capture regions, we do not advise using these samples until we have figured out the correct boundaries and changed the coverage data in annodb accordingly.

We have 592 samples downloaded from phs000473. Most have >90% CCDS covered at least 10x, similar to 65MB CHGV kits, while a minority have closer to 80% covered (this proportion may grow as we download more individuals with lowe coverage). The number of variants called in these samples is correlated with % CCDS covered as expected. The natural split between the two groups seems to be at about 85%. You can find sample files for phs000473 samples in various coverage bins here:

/nfs/goldstein/software/atav_home/data/sample/phs000473_590.txt
/nfs/goldstein/software/atav_home/data/sample/phs000473_590_ccdsbelow85.txt
/nfs/goldstein/software/atav_home/data/sample/phs000473_590_ccdsabove85.txt
/nfs/goldstein/software/atav_home/data/sample/phs000473_590_ccdsabove90.txt
/nfs/goldstein/software/atav_home/data/sample/phs000473_590_ccdsbelow90.txt

A list of artifacts for these samples will be posted when available.

More details on the QC of these samples is attached if you are interested.