From c48f0423d11f2ca01fc4647ada9586967c9c474a Mon Sep 17 00:00:00 2001 From: helrick Date: Thu, 26 Mar 2020 14:03:48 -0400 Subject: [PATCH] switching logic in denovo filters to use numerical --- cre.gemini2txt.vcf2db.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cre.gemini2txt.vcf2db.sh b/cre.gemini2txt.vcf2db.sh index 59bf168..0d84388 100755 --- a/cre.gemini2txt.vcf2db.sh +++ b/cre.gemini2txt.vcf2db.sh @@ -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