makeIGVbatch.sh

#!/bin/bash
#Input Format
#Family.ID       Child   Mother  Father  Flag    Variant.ID Gene.Name

IN=$1

awk '{print $2"\n"$3"\n"$4}' <(sed '1d' $IN) |uniq > $(dirname $IN)/$(basename ${IN%.*}).list

while read line; do  
    tmp=$(find \
        $(mysql --defaults-group-suffix=seqdb --defaults-file=/nfs/goldstein/software/Bioinformatics_Tools/generateVariantReport/.my.cnf -e "select AlignSeqFileLoc from seqdbClone where CHGVID = '$line' ;" |head -n2|tail -n1|sed 's/_temp[0-9]\?/18/') \
        -name '*final.bam')

    if [ -z "${tmp//\/\//\/}" ]
        then >&2 echo "ERROR: Did not find BAM for $line"
    elif [ $(du -sh $tmp|wc -l) -gt 1 ]
        then >&2 echo "ERROR: Found more than one BAM for $line"
             >&2 echo "$tmp"
    else
        echo "$(dirname $tmp)/$(basename $(readlink $tmp))"
    fi

done<$(dirname $IN)/$(basename ${IN%.*}).list > $(dirname $IN)/$(basename ${IN%.*}).bamloc

#sed 's/\/nfs/\\\\10.73.52.21/' $(dirname $IN)/$(basename ${IN%.*}).bamloc |sed 's/\//\\/g' > $(dirname $IN)/$(basename ${IN%.*}).bamwinloc
sed 's/\/nfs/\\\\10.73.52.21/' $(dirname $IN)/$(basename ${IN%.*}).bamloc |sed 's/homes\/svaprojects/homes/'|sed 's/10.73.52.21\/fastq\([0-9]\+\)/igm-avere.igm.cumc.columbia.edu\/fastq\1/' | sed 's/\//\\/g'|sed 's/\\\\ALIGNMENT/\\ALIGNMENT/g' > $(dirname $IN)/$(basename ${IN%.*}).bamwinloc
#sed 's/\/nfs/\\\\igm-avere.igm.cumc.columbia.edu/' $(dirname $IN)/$(basename ${IN%.*}).bamloc |sed 's/homes\/svaprojects/homes/' | sed 's/\//\\/g' > $(dirname $IN)/$(basename ${IN%.*}).bamwinloc

while read i
    do PRO_LOC=$(grep -w $(echo $i|awk '{print $2}') $(dirname $IN)/$(basename ${IN%.*}).bamwinloc|head -n1)
       if [ "$PRO_LOC" = "" ] ;then PRO_LOC="NA";fi
       DAD_LOC=$(grep -w $(echo $i|awk '{print $3}') $(dirname $IN)/$(basename ${IN%.*}).bamwinloc|head -n1)
       if [ "$DAD_LOC" = "" ] ;then DAD_LOC="NA";fi
       MOM_LOC=$(grep -w $(echo $i|awk '{print $4}') $(dirname $IN)/$(basename ${IN%.*}).bamwinloc|head -n1)
       if [ "$MOM_LOC" = "" ] ;then MOM_LOC="NA";fi
       VAR_CHR=$(echo $i|awk '{print $6}')
       VAR_LOC=$(echo $i|awk '{print $7}')
       VAR_GENE=$(echo $i|awk '{print $9}')
       PRO=$(echo $i|awk '{print $2}')
       echo "$PRO_LOC $DAD_LOC $MOM_LOC $VAR_CHR $VAR_LOC $((VAR_LOC-40)) $((VAR_LOC+40)) $PRO $VAR_GENE";done < <(sed 's/ /_/g' $IN|sed 's/-/\t/'|sed 's/-/\t/'|sed '1d'|sort -k6,6n) > $(dirname $IN)/$(basename ${IN%.*}).info.txt

       dir=$(pwd|sed 's/\/nfs/\\\\igm-avere.igm.cumc.columbia.edu/'|sed 's/home\/[^\/]*/igm-avere.igm.cumc.columbia.edu\/homes/'|sed 's/homes\/goldsteinlab/goldsteinlab/'|sed 's/homes\/svaprojects/svaprojects\/ns3116/'|sed 's/\//\\\\/g')
       awk -v dir="$dir" '{print "#"$8" "$4":"$5"\n""new\ngenome 1kg_v37\nload " $1"\nload " $2"\nload "$3"\nsnapshotDirectory \\"dir"\\IGV\ngoto "$4":"$6"-"$7"\nsort position\ncolor read strand\nsnapshot "$9"."$8"."$4"-"$5".png\ncollapse\nsnapshot "$9"."$8"."$4"-"$5".collapsed.png\n"}' $(dirname $IN)/$(basename ${IN%.*}).info.txt >$(dirname $IN)/$(basename ${IN%.*}).batch