Module_PedigreeCheck.sh

#!/bin/bash
#$ -cwd -V
#$ -pe smp 1
#$ -l h_vmem=1G
#$ -e ~/log
#$ -o ~/log

source ~/.bash_profile

#-------------------------------------------------------------------------------------------#
#  Author      : Andrew J Skelton                                                           |
#  Language    : Bash                                                                       |
#  Study       : Exome Project                                                              |
#  Data Owner  : Newcastle University - Prof. Sophie Hambleton                              |
#  Type        : Gateway Script                                                             |
#  Description : Create PED File from Filemap, and Check for sample's existence             |
#  Version     : 1.0                                                                        |
#  Input       : Base Directory to Batch Preprocessing Directory                            |
#  Input       : Path to Reference Files                                                    |
#  Input       : Log Output Folder                                                          |
#-------------------------------------------------------------------------------------------#



##'Create Folder Structure and output File
##'-----------------------------------------------------------------------------------------#
mkdir -p ${3}
LOG=${3}PedigreeCheck.log
PED=${2}Samples.ped
##'-----------------------------------------------------------------------------------------#



##'Check if Log File Exists
##'-----------------------------------------------------------------------------------------#
if ls ${LOG} 1> /dev/null 2>&1; then
  echo "*** New Run ***" >> ${LOG}
else
  touch ${PED}
  echo "*** New Run ***" >> ${LOG}
fi
##'-----------------------------------------------------------------------------------------#



##'Check if PED File Exists
##'-----------------------------------------------------------------------------------------#
if ls ${PED} 1> /dev/null 2>&1; then
  echo "Ped File Exists, deleting old version" >> ${LOG}
  rm ${PED}
fi
touch ${PED}
echo "Created Ped File" >> ${LOG}
##'-----------------------------------------------------------------------------------------#



##' Loop through Samples in filemap
##' Check if P/Maternal Sample Exists
##'   False: Set Entry to 0
##' Recode for Gender
##' Check if File Exists
##'   True: Make Ped Entry
##'   False: Add to Log
##'-----------------------------------------------------------------------------------------#
while read line
do
  FAM_ID=$(echo "${line}" | cut -f 1)
  SAM_ID=$(echo "${line}" | cut -f 2)
  PROBAN=$(echo "${line}" | cut -f 6)
  PAT_ID=$(echo "${line}" | cut -f 3)
  MAT_ID=$(echo "${line}" | cut -f 4)

  # Check Paternal Sample Exists
  PAT_QUERY=`find ${1} -type f -name "${PAT_ID}.g.vcf" | wc -l`
  if (( PAT_QUERY == 0 )); then
    echo "Pedigree Error: ${SAM_ID} is part of ${FAM_ID}, ${PAT_ID} Not Found, setting to 0" >> ${LOG}
    PAT_ID="0"
  fi

  # Check Maternal Sample Exists
  MAT_QUERY=`find ${1} -type f -name "${MAT_ID}.g.vcf" | wc -l`
  if (( MAT_QUERY == 0 )); then
    echo "Pedigree Error: ${SAM_ID} is part of ${FAM_ID}, ${MAT_ID} Not Found, setting to 0" >> ${LOG}
    MAT_ID="0"
  fi

  # Recode for Gender
  if [ $(echo "${line}" | cut -f 5) = "M" ]; then
    SEX="1"
  else
    SEX="2"
  fi

  # Check if File Exists
  query_list=`find ${1} -type f -name "${SAM_ID}.g.vcf" | wc -l`
  if (( query_list > 0 )); then
    echo -e "${FAM_ID}\t${SAM_ID}\t${PAT_ID}\t${MAT_ID}\t${SEX}\t${PROBAN}" >> ${PED}
  else
    if [[ ${FAM_ID} == "FAM"* ]]; then
      echo "Sample Missing: *WARNING* ${SAM_ID} is part of ${FAM_ID}" >> ${LOG}
    else
      echo "Sample Missing: ${SAM_ID}" >> ${LOG}
    fi
  fi

done < ${2}SampleMap.txt
##'-----------------------------------------------------------------------------------------#