From cc9b1934dd2f978fcbc1b9571940544dbdd97dca Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Fri, 12 Apr 2019 23:51:38 -0400
Subject: [PATCH] ROH, ROHET naive analysis

---
 cre.roh.naive.sh   |  6 ++--
 cre.rohet.naive.sh | 79 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 82 insertions(+), 3 deletions(-)
 create mode 100755 cre.rohet.naive.sh

diff --git a/cre.roh.naive.sh b/cre.roh.naive.sh
index d9d8b0b..cb27163 100755
--- a/cre.roh.naive.sh
+++ b/cre.roh.naive.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # runs of HOM MAF 5% variant in proband (CH0620) affected sib (CH0621) and in both
 # filters DP=50, QUAL>=500
-# gt_types=0=HOM_REF or 3 = HOM_ALT, 1 = HET
+# gt_types=0=HOM_REF or 3 = HOM_ALT, 1 = HET, 2 - no call
 # usage:
 # cre.roh.naive.sh sample gemini.db [maf=0.05]
 # output:
@@ -11,7 +11,7 @@
 sample=$1
 echo "chrom,pos,ref,alt,impact,qual,dp,gene,maf,gts."$sample",gt_types."$sample",gt_alt_depths."$sample",stretch_length_variants,stretch_length_bp,stretch_id,stretch_genes" | tee $sample.roh_variants.tsv
 
-maf=1
+maf=0.05
 if [ -n "$3" ]
 then
     maf=$3
@@ -60,7 +60,7 @@ BEGIN{
     prev=genotype;
     prev_chrom=$1;
     print $0","stretch_length_variants","stretch_length_bp","stretch_id",\""stretch_genes"\"";
-}' | grep -v "0$" | awk -F ',' '{ if ($13>9) print $0;}' \
+}' | grep -v "0$" | awk -F ',' '{ if ($13>5) print $0;}' \
 | sort -t "," -k1,1 -k15,15n \
 | awk -F "," '
 BEGIN{
diff --git a/cre.rohet.naive.sh b/cre.rohet.naive.sh
new file mode 100755
index 0000000..6e55a66
--- /dev/null
+++ b/cre.rohet.naive.sh
@@ -0,0 +1,79 @@
+#!/bin/bash
+# runs of HETEROZYGOUS VARIANTS MAF 5% variant in proband (CH0620) affected sib (CH0621) and in both
+# filters DP=50, QUAL>=500
+# gt_types 1 = HET
+# usage:
+# cre.roh.naive.sh sample gemini.db [maf=0.05]
+# output:
+# - sample.roh_variants.tsv - list of variants, print with tee for debugging
+# - stdout: list of ROH
+
+sample=$1
+echo "chrom,pos,ref,alt,impact,qual,dp,gene,maf,gts."$sample",gt_types."$sample",gt_alt_depths."$sample",stretch_length_variants,stretch_length_bp,stretch_id,stretch_genes" | tee $sample.roh_variants.tsv
+
+maf=0.05
+if [ -n "$3" ]
+then
+    maf=$3
+fi
+
+gemini query -q "select chrom,start+1 as pos, ref, alt,impact,qual,depth, gene, max_aaf_all as maf, gts."$sample",gt_types."$sample",gt_alt_depths."$sample" from variants where
+type='snp' and depth>=10 and qual>=100 and max_aaf_all<="$maf --gt-filter "gt_types."$sample" != 2" $2 | sed s/"\t"/","/g | sort -t "," -k1,1n -k2,2n \
+| tee -a $sample.roh_variants.tsv | awk -F "," '
+BEGIN{
+    prev=1;
+    prev_gene="";
+    prev_chrom="";
+    stretch_length_variants=0;
+    stretch_length_bp=0;
+    stretch_id="";
+    stretch_genes="";
+}
+{
+    genotype=$11;
+    if(genotype != 1 || $1 != prev_chrom){
+	stretch_length_variants=0;
+	stretch_length_bp=0;
+	stretch_id=0;
+	stretch_genes="";
+	prev_gene="";
+    }else{
+        if(prev==0){
+	    stretch_length_variants=stretch_length_variants+1;
+	    stretch_length_bp=$2-stretch_id+1;
+	    if ($8 != prev_gene && $8 != ""){
+    		stretch_genes=stretch_genes","$8;
+    	    }
+    	    prev_gene=$8;
+	}else{
+    	    stretch_length_variants=1;
+    	    stretch_id=$2;
+    	    stretch_length_bp=$2-stretch_id+1;
+    	    stretch_genes=$8;
+    	    prev_gene=$8;
+	};
+    }
+    prev=genotype;
+    prev_chrom=$1;
+    print $0","stretch_length_variants","stretch_length_bp","stretch_id",\""stretch_genes"\"";
+}' | grep -v "0$" | awk -F ',' '{ if ($13>=10) print $0;}' \
+| sort -t "," -k1,1 -k15,15n \
+| awk -F "," '
+BEGIN{
+    prev_chr="";
+    prev_stretch_id="";
+    prev_stretch="";
+}
+{
+    if($1 != prev_chr){
+	print prev_stretch;
+    }else{
+	if (prev_stretch_id != $15){
+	    print prev_stretch;
+	}
+    }
+    prev_stretch=$0;
+    prev_chr=$1;
+    prev_stretch_id=$15;
+}' | grep -v "^$"
+