Replace numeric genotype code with DNA letter

Question

how can i replace the numeric genotype code with a DNA letter? i have a modified vcf file that looks like that:

POS REF ALT A2.bam C10.bam 448 T C 0/0:0,255,255 0/0:0,255,255 2402 C T 1/1:209,23,0 xxx:255,0,255 n...

i want to replace the 0/0 with the ref letter, 1/1 with the alt letter and delete all the string after it. it should look like this:

POS REF ALT A2.bam C10.bam 448 T C T T 2402 C G G xxx n...

been trying to do it with sed but it didn't work don't know how to approach it

Answer 1

Would you please try:

awk '{
    if (NR > 1) {
        for (i=4; i<=5; i++) {
            split($i, a, ":")
            $i = a[1]
            if ($i == "0/0") $i = $2
            if ($i == "1/1") $i = $3
        }
    }
    print
}' file.txt

Output:

POS  REF ALT     A2.bam C10.bam
448 T C T T
2402 C T T xxx
n...    

• The for loop processes the 4th and 5th columns (A2.bam and C10.bam).
• First it chops off the substring after ":".
• If the remaining value is equal to "0/0", then replace it with the 2nd column (REF).
• In case of "1/1", use the 3rd column (ALT).

Hope this helps.