Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

switching logic in denovo filters to use numerical #2

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

switching logic in denovo filters to use numerical #2

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions cre.gemini2txt.vcf2db.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,9 +100,9 @@ then
mom=`gemini query -q "select name from samples where phenotype=1 and sex=2" $file`
dad=`gemini query -q "select name from samples where phenotype=1 and sex=1" $file`

s_gt_filter="gt_types."$proband" == HET and gt_types."$dad" == HOM_REF and gt_types."$mom" == HOM_REF"
#(gt_types."$proband" == HOM_ALT and gt_types."$dad" == HOM_REF and gt_types."$mom" == HET)"
# otherwise a lot of trash variants
s_gt_filter="gt_types."$proband" == 1 and (gt_types."$dad" == 0 or gt_types."$dad" == 3) and (gt_types."$mom" == 0 or gt_types."$mom" == 3)"

# otherwise a lot of trash variants
sQuery=$sQuery" and qual>=500"
gemini query -q "$sQuery" --gt-filter "$s_gt_filter" --header $file
else
Expand Down