Excluding undetermined index reads

prepare_bcbio_config_crf.sh

@@ -52,7 +52,7 @@ perl -pi -e 's/\r//' $PROJECT_ID.ped
 mkdir -p $READS_DIR/$PROJECT_ID
 
 # generate the family_ids list - makes strong assumption about relative paths!
-ls ../../data/$PROJECT_ID/*.gz | cut -d '/' -f 5 | cut -f 1,3 -d '_' | sort -u > $PROJECT_ID.family_ids.txt
+ls ../../data/$PROJECT_ID/*.gz | grep -v Undetermined | cut -d '/' -f 5 | cut -f 1,3 -d '_' | sort -u > $PROJECT_ID.family_ids.txt
 
 PLATE_ID=`cut -f 1 -d '_' $PROJECT_ID.family_ids.txt | sort -u`
 for FAMILY_ID in `cut -f 2 -d '_' $PROJECT_ID.family_ids.txt`

prepare_bcbio_config_santosh.sh

@@ -66,7 +66,7 @@ do
 
     for FILE in `ls $DOWNLOAD_DIR/$PROJECT_ID/*${SAMPLE}*.gz`
     do
-      echo "$FILE,${SAMPLE}_${FAMILY_ID},$FAMILY_ID,$SEX,$PHENOTYPE,$TARGET" >> ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
+      echo "$FILE,${SAMPLE},$FAMILY_ID,$SEX,$PHENOTYPE,$TARGET" >> ${VERSION}_${PROJECT_ID}_${FAMILY_ID}.csv
     done
 
   done