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Bash to update files to be used by awk
10-03-2016
F13_epilepsy_filtered_comparison.txt
F13_epilepsy_filtered.vcf
chr1 43395635 43395635 C T exonic SLC2A1 . synonymous SNV SLC2A1:NM_006516:exon5:c.588G>A:p.P196P rs2229682 0.23 0.12 0.024 0.21 0.08 0.19 0.15 0.18 0.044 0.19 0.074 0.23 0.21 0.19 0.19 0.15 0.049 0.2 0.12 -0.1558 -0.594 . . . . . . . . . . . . Benign not_specified RCV000081436.5 MedGen CN169374 GOOD 399 het 19
#!/bin/bash
for FN in /home/cmccabe/Desktop/comparison/ref_val/*.txt; do
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 $50 OFS $51 OFS $52 OFS $53
}
END {for(j = 1; j <= ic; j++)
print o[i[j]] > outfile
}' $FN ${FN%%_*}/home/cmccabe/Desktop/comparison/validation/files/*.vcf
doneMatch: 9943666 C T 161281245 T C 138662273 G A 64142859 C T
Match: chr16 9943666 C T exonic GRIN2A GOOD 343 het 18 chr5 161281245 T C exonic GABRA1 GOOD 197 het 13 chr9 138662273 G A exonic KCNT1 GOOD 275 het 15 chr3 64142859 C T exonic PRICKLE2 GOOD 355 het 23
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