I have the following testfile.txt:
CHROM POS REF ALT DP POS N_ALLELES N_CHR {REF} {ALT}
chr1 16495 G C 252 16495 2 2 0.5 0.5
chr1 16719 T A 189 16719 2 2 0.5 0.5
chr1 16841 G T 521 16841 2 2 0.5 0.5
chr1 17626 G A 124 17626 2 2 0.5 0.5
chr1 17697 G C 63 17697 2 2 0.5 0.5
chr1 19004 A G 13 19004 2 2 0.5 0.5
chr1 69270 A G 20 69270 2 2 0 1
chr1 69511 A G 240 69511 2 2 0 1
chr1 69897 T C 28 69897 2 2 0 1
I am trying to execute an awk command to add a new column based on the information from the text file but the following code is only working on the first conditions:
awk '{
if ($9 == 0.5 && $10 == 0.5 && $7 == 2) {
print $0"\thet";
} else if (($9 == 0 && $10 == 0.5 && $7 == 3) || ($9 == 0.5 && $10 == 0 && $7 == 3)) {
print $0"\t"het2;
} else if (($9 == 0 && $10 == 1 && $7 == 2) || ($9 == 1 && $10 == 0 && $7 == 2)){
print $0"\t"hom;
}
}' testfile.txt
And the output that I am obtaining is the following:
chr1 16495 G C 252 16495 2 2 0.5 0.5 het
chr1 16719 T A 189 16719 2 2 0.5 0.5 het
chr1 16841 G T 521 16841 2 2 0.5 0.5 het
chr1 17626 G A 124 17626 2 2 0.5 0.5 het
chr1 17697 G C 63 17697 2 2 0.5 0.5 het
chr1 19004 A G 13 19004 2 2 0.5 0.5 het
chr1 69270 A G 20 69270 2 2 0 1
chr1 69511 A G 240 69511 2 2 0 1
chr1 69897 T C 28 69897 2 2 0 1
chr1 120983 C T 35 120983 2 2 0.5 0.5 het
Can someone please explain me why my awk command is not working ?
Thanks in advance.
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