Making pattern of GT:AD:DP:PL column values to be replaced by o and 1.

Question

[S AR]

Im trying to replace GT:AD:DP:GQ:PL values from all samples in a multi vcf file with 1.

My file looks like this:

Pos 6620    6734    6737    6742    6750    7151    7212    7362
Alt A   A   A   G   GC  A   T   G
ERR038741   0   1:1,213:214:99:7391,0   0   0   0   0   1:2,205:207:99:7078,0   1:0,191:191:99:7383,0
ERR040140   0   1:1,336:337:99:11415,0  0   0   0   0   0   0
ERR046796   0   1:4,180:184:99:5672,0   0   0   1:3,182:185:99:6609,0   0   0   0
ERR046903   0   1:1,170:171:99:6142,0   0   0   1:1,158:159:99:5954,0   0   0   0
ERR067581   0   1:0,86:86:99:3037,0 0   0   0   0   0   0
ERR067593   0   1:0,90:90:99:3229,0 0   0   0   0   0   0
ERR067606   0   1:0,65:65:99:2267,0 0   0   0   0   1:0,58:58:99:1971,0 1:0,62:62:99:2353,0
ERR067607   0   1:0,73:73:99:2593,0 0   0   0   0   0   0
ERR067608   0   1:0,70:70:99:2390,0 0   0   0   0   0   0
ERR067609   0   1:0,80:80:99:2826,0 0   0   0   0   1:0,75:75:99:2574,0 1:1,82:83:99:3049,0

I want the "1:0,73:73:99:2311,0: type of text to be replaced with 1. I m able to pick the pattern but how to replace it with one. The grep command for pattern matching is:

grep "1:0,.*" susc_ml_combine.vcf

Now how to replace it? can any one help please.

[Susmita Mandal]

Did you try using awk?

[S AR]

i tried gsub from R but it didnt work.

As well i tried:

ex -s -c '%1:1,.*/1/g|x' file.vcf

Answer 1

[Kevin Blighe]

Just use sed on your command line:

cat temp 
Pos 6620    6734    6737    6742    6750    7151    7212    7362
Alt A   A   A   G   GC  A   T   G
ERR038741   0   1:1,213:214:99:7391,0   0   0   0   0   1:2,205:207:99:7078,0   1:0,191:191:99:7383,0
ERR040140   0   1:1,336:337:99:11415,0  0   0   0   0   0   0
ERR046796   0   1:4,180:184:99:5672,0   0   0   1:3,182:185:99:6609,0   0   0   0
ERR046903   0   1:1,170:171:99:6142,0   0   0   1:1,158:159:99:5954,0   0   0   0
ERR067581   0   1:0,86:86:99:3037,0 0   0   0   0   0   0
ERR067593   0   1:0,90:90:99:3229,0 0   0   0   0   0   0
ERR067606   0   1:0,65:65:99:2267,0 0   0   0   0   1:0,58:58:99:1971,0 1:0,62:62:99:2353,0
ERR067607   0   1:0,73:73:99:2593,0 0   0   0   0   0   0
ERR067608   0   1:0,70:70:99:2390,0 0   0   0   0   0   0
ERR067609   0   1:0,80:80:99:2826,0 0   0   0   0   1:0,75:75:99:2574,0 1:1,82:83:99:3049,0


sed 's/ \+/\t/g' temp | sed 's/1:0,[0-9\\:\\,]*/1/g'
Pos 6620    6734    6737    6742    6750    7151    7212    7362
Alt A   A   A   G   GC  A   T   G
ERR038741   0   1:1,213:214:99:7391,0   0   0   0   0   1:2,205:207:99:7078,0   1
ERR040140   0   1:1,336:337:99:11415,0  0   0   0   0   0   0
ERR046796   0   1:4,180:184:99:5672,0   0   0   1:3,182:185:99:6609,0   0   0   0
ERR046903   0   1:1,170:171:99:6142,0   0   0   1:1,158:159:99:5954,0   0   0   0
ERR067581   0   1   0   0   0   0   0   0
ERR067593   0   1   0   0   0   0   0   0
ERR067606   0   1   0   0   0   0   1   1
ERR067607   0   1   0   0   0   0   0   0
ERR067608   0   1   0   0   0   0   0   0
ERR067609   0   1   0   0   0   0   1   1:1,82:83:99:3049,0