Set up and pre-processing for shared affected proband analysis

docs/run-notes/19373_run_notes.md

@@ -89,4 +89,74 @@ qsub -v PLATE_ID=${PLATE_ID},PROJECT_ID=${PROJECT_ID},VERSION_N=${VERSION_N} -J
 
 # Shared affected analysis
 
-Changed father for 20211005_Ansari_Morad_19373_438214 back to affected in params family PED file
+Changed father for 20211005_Ansari_Morad_19373_438214 back to affected in params family PED file and in PED version.
+
+## Set-up
+
+```
+export SOURCE_DIR=/scratch/u035/project/trio_whole_exome/analysis/output
+export BATCH_ID=20211005_Ansari_Morad
+export BATCH_NUM=20211005
+export PLATE_ID=19373
+export VERSION_N=v1
+export PROJECT_ID=20211006_19373_438214
+export SOURCE_DIR=${SOURCE_DIR}/${VERSION_N}_${BATCH_NUM}
+/home/u035/project/scripts/NHS_WES_trio_setup.sh &> v1_20211005_Ansari_Morad.NHS_WES_trio_setup.log
+mv v1_20211005_Ansari_Morad.NHS_WES_trio_setup.log ../20211006_19373_438214/LOG/
+```
+
+## Remove other families & copy DECIPHER id map
+
+```
+cd ../20211006_19373_438214
+cp ../20211006_19373/DECIPHER_INTERNAL_IDs.txt ./
+```
+
+Edit `DECIPHER_INTERNAL_IDs.txt` to remove other families.
+
+```
+cd PED
+rm 20211005_Ansari_Morad_19373_438169.ped 20211005_Ansari_Morad_19373_438236.ped 20211005_Ansari_Morad_19373_451595.ped
+cd ../VCF/
+rm 19373_438169-gatk-haplotype-annotated.vcf.gz 19373_438236-gatk-haplotype-annotated.vcf.gz 19373_451595-gatk-haplotype-annotated.vcf.gz 
+```
+
+## Pre-processing
+
+```
+BATCH_ID=20211005_Ansari_Morad
+PLATE_ID=19373
+FAMILY_ID=438214
+cd /scratch/u035/project/trio_whole_exome/analysis/20211006_19373_438214/PED
+cp ${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.ped ${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.full.ped
+```
+
+Edited PED file to only affected individuals (child & father)
+
+```
+19373_438214    130221_438214   0   0   1	2
+19373_438214    130220_438214   0	0	1	2
+```
+
+Copy and pre-process VCF files
+
+```
+cd ../VCF
+mv 19373_438214-gatk-haplotype-annotated.vcf.gz 19373_438214-gatk-haplotype-annotated.full.vcf.gz
+tabix 19373_438214-gatk-haplotype-annotated.vcf.gz
+
+GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+REF_GENOME=/home/u035/project/resources/hg38.fa
+aff_kid_1_id=130221
+aff_kid_2_id=130220
+
+time java -Xmx24g -jar ${GATK3} -T SelectVariants \
+-R ${REF_GENOME} \
+-V ${PLATE_ID}_${FAMILY_ID}-gatk-haplotype-annotated.full.vcf.gz \
+-sn ${aff_kid_1_id}_${FAMILY_ID} \
+-sn ${aff_kid_2_id}_${FAMILY_ID} \
+-jdk_deflater \
+-jdk_inflater \
+-o ${PLATE_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz  \
+-env
+```