Changed sort order of families by batch instead of date, added steps for...

Changed sort order of families by batch instead of date, added steps for setting parent field to 0 for shared-affected families, description of step for DECIPHER upload file copy

docs/SOP_reanalysis_preparation.md

@@ -130,14 +130,10 @@ cut -f 5 families.txt | sort | uniq -d > families_multiple_entries.txt
 rm family_entries_removed_from_reanalysis.txt 2> /dev/null
 for family in `cat families_multiple_entries.txt`
 do
-  grep $family$ families.txt | sort | sed -e 's/\t/\_/g' > $family.txt
+  grep $family$ families.txt | sort -k4 -n | sed -e 's/\t/\_/g' > $family.txt
   count=`wc -l $family.txt | awk '{ print $1 - 1 }'`
-  for ((i = 1; i <= $count; i = i + 1))
-  do
-    family_entry=`head -n $i $family.txt | tail -n 1`
-    echo $family_entry >> family_entries_removed_from_reanalysis.txt
-  done
-  rm $family.txt
+  head -n $count $family.txt >> family_entries_removed_from_reanalysis.txt
+#  rm $family.txt
 done
 
 cd ../families
@@ -147,6 +143,7 @@ ls | grep -v trio | grep -v duo | sed -e 's/\_/\t/g' | cut -f 2-5 | sed -e 's/\t
 
 5. Pull in all the relevant PED files into the params folder
 
+```
 cd ../params
 mkdir all
 count=`wc -l all.txt | awk '{ print $1 }'`
@@ -157,6 +154,7 @@ do
 
   cp ../../$project/params/*$family*.ped ./all/
 done
+```
 
 6. Make folders for the relevant groups and sort the families based on their PED files
 
@@ -186,3 +184,21 @@ do
   done
 done
 ```
+
+7. Ensure all parent fields are set to 0 for the shared-affected families
+
+```
+cd shared_affected
+for file in *.ped
+do
+  awk '{ print $1 "\t" $2 "\t0\t0\t" $5 "\t" $6 }' $file > temp.out
+  mv temp.out $file
+done
+```
+
+8. Copy DECIPHER upload files from previous analyses. If multiple files are possible, select in preference order:
+
+a. <INDI>_<FAM>_DECIPHER_v11.xlsx (the best)
+b. <INDI>_<FAM>_DECIPHER_v10.xlsx (if we do not have v11 version)
+c. <INDI>_<FAM>_DEC_FLT.csv (least preferred, if we do not have a xlsx version -> this was the case at the beginning of the NHS Trio WES service)
+