04_CheckRelatedness.sh

#!/bin/bash
## because our sample is mixed ethnicity this looks funky return to after checking ethnicity.

## EXECUTION
# sh 02_CheckRelatedness.sh

## REQUIRES the following files
# ${PROCESSDIR}/QCData/${FILEPREFIX}_QCd

## REQUIRES the following software
# king, plink, R

## INPUT
# ${PROCESSDIR}/QCData/${FILEPREFIX}_QCd # binary plink files following prelim QC

## OUTPUT
# ibd.png HisMeanKinshipCoefficients.pdf

echo "checking the arguments for config file----------------------------------------------------------------------------"
datapeth=$1

if [ -z "$1" ]
then
        echo "No argument supplied"
        echo "Please input the paht of the data folder as the first argument"
		exit 1 # fail
fi


echo "running the check relatedness at $datapeth"
source ${datapeth}/config
touch "$logfile_04"
exec > >(tee "$logfile_04") 2>&1
cd ${PROCESSDIR}/CheckRelatedness || exit

check_relatedness () {

   echo "Check the relatedeness for each population--------------------------------------------------------------------------"

   ${PLINK}/plink --bfile ${PROCESSDIR}/CheckEthnicity/ToBeChecked \
                  --keep $1 \
                  --make-bed \
                  --allow-no-sex \
                  --out ${FILEPREFIX}_${2}_QCd

   ## check for relatedness with other samples with KING
   "$KINGPATH"/king -b ${FILEPREFIX}_${2}_QCd.bed \
                     --kinship \
                     --prefix ${FILEPREFIX}_${2}_QCd_kingship

   Rscript ${SCRIPTDIR}/4_Resources/plotKinshipCoeff.r \
                     ${FILEPREFIX}_${2}_QCd_kingship.kin0 \
                     ${DATADIR}/3_Results/04 \
                     $2

   ## check for relatedness with other samples with plink
   ${PLINK}/plink --bfile ${FILEPREFIX}_${2}_QCd \
                  --genome \
                  --mind 0.2 \
                  --out ${FILEPREFIX}_${2}_QCd_ibd

   Rscript ${SCRIPTDIR}/4_Resources/Plot_ibd.r ${FILEPREFIX}_${2}_QCd_ibd.genome ${DATADIR}/3_Results/04 $2

   rm ${FILEPREFIX}_${2}_QCd*


}


if [ -z "$2" ]
then
   populations=($(cut -f3 --delim="," ${DATADIR}/3_Results/03/PredictedPopulations.csv | tail -n +2 | sort | uniq))

   for each in "${populations[@]}"
   do
      grep ${each} ${DATADIR}/3_Results/03/PredictedPopulations.csv | cut -f1-2 --delim="," --output-delimiter=" " > ${each}Samples.txt
      
      if [[ $(wc -l <${each}Samples.txt) -ge 1 ]]
      then
         echo "Checking the relatedness on ", ${each}, "population."
         check_relatedness ${each}Samples.txt ${each}
      fi
   done 

else

   grep $population ${DATADIR}/3_Results/03/PredictedPopulations.csv | cut -f1-2 --delim="," --output-delimiter=" " > ${population}Samples.txt
   echo "Checking the relatedness on ", ${population}, "population."
   check_relatedness  ${population}Samples.txt  ${population}

fi