mjhjmtu

I have a challenge with probably a stupid thing, please be patient with me! I have a large file (tab-delimited) that its head is like below: (Here, Flags column is empty, but not in the original file, so it has to be kept. I guess this column and the next columns that there is space in their name caused the problem).

countChromosome Start Stop Ref/Alt Identifier Flags Read Depth (DP) Allele Counts Allele Frequencies # Alleles # Het # HomoVar AMR - Allele Counts AMR - Allele Frequencies AMR - # Alleles
1 10177 10177 -/C rs367896724 103152 2130 0.425319 5008 1490 320 250 0.360231 694
1 10235 10235 -/A rs540431307 78015 6 0.00119808 5008 6 0 1 0.00144092 694
1 10352 10352 -/A rs555500075 88915 2191 0.4375 5008 2025 83 285 0.410663 694
1 10504 10505 A/T rs548419688 9632 1 0.000199681 5008 1 0 0 0 694
1 10505 10506 C/G rs568405545 9676 1 0.000199681 5008 1 0 0 0 694
1 10510 10511 G/A rs534229142 9869 1 0.000199681 5008 1 0 1 0.00144092 694
1 10538 10539 C/A rs537182016 9203 3 0.000599042 5008 3 0 1 0.00144092 694

I tried to get information of some columns for a given list of Identifier in the text file as below:

rs555500075
rs548419688
rs568405545
rs534229142

I used this command:

fgrep -wf ids.txt original_file.txt | awk ' print $1"t"$2"t"$4"t"$5"t"$8"t"$9"t"$13' > test1

But the output of the above command is like:

countChromosome Start Ref/Alt Identifier Depth (DP) Frequencies
1 10352 -/A rs555500075 0.4375 5008 0.410663
1 10504 A/T rs548419688 0.000199681 5008 0
1 10505 C/G rs568405545 0.000199681 5008 0
1 10510 G/A rs534229142 0.000199681 5008 0.00144092

As I mentioned above, I guess Flag column (6th column) and the next columns that there is space in their name caused the problem. Although, I tried some way to solve the issue, none of them was useful. Could you please kindly help me out to solve this problem?

Many thanks in advance