metal.sh

# 25-3-2020 JHZ

export SomaLogic=/home/jhz22/SomaLogic
export sumstats=$SomaLogic/sumstats
export METAL=$SomaLogic/METAL

## generation of protein-specific METAL entries

if [ ! -d $METAL ]; then mkdir $METAL; fi
(
for study in FHS INTERVAL KORA Malmo QMDiab TwinsUK
do
   ls $sumstats/$study | sed 's/'"$study".'//g' | awk -vstudy=$study '{
      s=$1;gsub(/.gz|@/,"",s);
      p=s;gsub(/\.txt/,"",p);
      print p " " ENVIRON["sumstats"] "/" study "/" study "." s ".gz"
   }'
done
) | \
awk '{print $0, NR}' > METAL/METAL.tmp

sort -k1,1 $METAL/METAL.tmp > $METAL/METAL.list
for p in $(cat doc/SomaLogic.list | tr '\n' ' ')
do
  (
     echo SEPARATOR TAB
     echo COLUMNCOUNTING STRICT
     echo CHROMOSOMELABEL CHR
     echo POSITIONLABEL POS
     echo CUSTOMVARIABLE N
     echo LABEL N as N
     echo TRACKPOSITIONS ON
     echo AVERAGEFREQ ON
     echo MINMAXFREQ ON
     echo ADDFILTER CODE_ALL_FQ ">=" 0.001
     echo ADDFILTER CODE_ALL_FQ "<=" 0.999
     echo MARKERLABEL SNPID
     echo ALLELELABELS EFFECT_ALLELE REFERENCE_ALLELE
     echo EFFECTLABEL BETA
     echo PVALUELABEL PVAL
     echo WEIGHTLABEL N
     echo FREQLABEL CODE_ALL_FQ
     echo STDERRLABEL SE
     echo SCHEME STDERR
     echo GENOMICCONTROL OFF
     echo LOGPVALUE ON
     echo OUTFILE $HOME/SomaLogic/METAL/$p- .tbl
     echo $p | \
     join METAL/METAL.list - | \
     sort -k3,3n | \
     awk '{print "PROCESS", $2}'
     echo ANALYZE HETEROGENEITY
     echo CLEAR
  ) > METAL/$p.metal
done

## all in one directory to get ready for QCGWAS

if [ ! -d $sumstats/work ]; then mkdir $sumstats/work; fi
parallel --env sumstats -j10 -C' ' 'ln -vsf {} $sumstats/work/$(basename {})' ::: $(cut -d' ' -f2 $METAL/METAL.tmp)

sbatch metal.sb