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Print . in blank fields to prevent fields from shifting
10-21-2016
.for file in /home/cmccabe/Desktop/concordance/comparison/update/*.txt ; do
file1=${file##*/} # Strip off directory
getprefix=${file1%%_*.txt}
file1=$(printf '%s\n' "/home/cmccabe/Desktop/concordance/reference/files/${file1%%_*.txt}_"*.txt) # look for matching file
if [[ -f "$file1" ]]
then
awk '
BEGIN {FS = OFS = "\t"
}
NR == 1 {
outfile = FILENAME
}
FNR == NR {
o[i[++ic] = $1 OFS $2 OFS $3] = $0
}
{if($2 OFS $4 OFS $5 in o)
o[$2 OFS $4 OFS $5] = $1 OFS $2 OFS $4 OFS $5 OFS $6 OFS $7 OFS $8 OFS $9 OFS $10 OFS $11 OFS $12 OFS $13 OFS $14 OFS $15 OFS $16 OFS $17 OFS $18 OFS $19 }
END {for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' $file $file1
fi
doneMissing in IDP but found in Reference: 2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5139C>T]+[=] 52.94 Not low found 12 52200340 A C exonic SCN8A 4129 28.3 1560;1672 413;453 0;0 0;0 0;2 31;0 c.[5070A>C]+[=] 20.97 Not low Not found 13 77570076 - A exonic CLN5 2762 26.6 2060;702 0;0 0;0 0;0 2050;696 0;0 c.526_527insA 99.42 TP Not low Not found 7 148106478 - GT intronic CNTNAP2 4051 28.5 0;1 0;0 0;0 2220;1829 1085;887 0;1 rs60451214 c.3716-5_3716-4insGT 48.68 Not low Not found 9 138678036 TGCCC - intronic KCNT1 834 23.1 0;0 0;0 0;31 0;1 0;0 0;802 rs141359570 c.3178-7_3178-3delTGCCC 96.16 Not low Not found 7 148106476 - TT intronic CNTNAP2 4052 28.8 0;0 5;0 0;0 2221;1826 1081;884 0;0 rs61232377 c.3716-7_3716-6insTT 48.49 Not low Not found 2 166245425 C T exonic SCN2A 49 12.6 0;0 13;9 0;0 18;9 0;0 0;0 c.[5109C>T]+[=] 55.1 Not low found
Missing in IDP but found in Reference: CHR POS REF ALT FUNC GENE COVERAGE PHRED A[#F,#R] C[#F,#R] G[#F,#R] T[#F,#R] INS[#F,#R] DEL[#F,#R] SNP MUT FREQ SANGER REGION TVC 2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 . c.[5139C>T]+[=] 52.94 . Not low found 12 52200340 A C exonic SCN8A 4129 28.3 1560;1672 413;453 0;0 0;0 0;2 31;0 . c.[5070A>C]+[=] 20.97 . Not low Not found 13 77570076 - A exonic CLN5 2762 26.6 2060;702 0;0 0;0 0;0 2050;696 0;0 . c.526_527insA 99.42 TP Not low Not found 7 148106478 - GT intronic CNTNAP2 4051 28.5 0;1 0;0 0;0 2220;1829 1085;887 0;1 rs60451214 c.3716-5_3716-4insGT 48.68 . Not low Not found 9 138678036 TGCCC - intronic KCNT1 834 23.1 0;0 0;0 0;31 0;1 0;0 0;802 rs141359570 c.3178-7_3178-3delTGCCC 96.16 . Not low Not found 7 148106476 - TT intronic CNTNAP2 4052 28.8 0;0 5;0 0;0 2221;1826 1081;884 0;0 rs61232377 c.3716-7_3716-6insTT 48.49 . Not low Not found 2 166245425 C T exonic SCN2A 49 12.6 0;0 13;9 0;0 18;9 0;0 0;0 . c.[5109C>T]+[=] 55.1 . Not low found
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