I got a vcf file (header and individual ID have been removed form the vcf file), which contains only genotype information for 1000 positions, looks like this (for the fist position)

    head all_unique.vcf
    
        5	49444858	rs12513792	C	A	100	PASS	AC=3353;AF=0.669529;AN=5008;NS=2504;DP=17854;EAS_AF=0.5625;AMR_AF=0.7075;AFR_AF=0.7489;EUR_AF=0.672;SAS_AF=0.6431;AA=.|||;VT=SNP	GT	0|1	1|0	0|1	1|0	0|1	0|1	1|1	1|0	1|0	1|1	1|1	1|0	0|1	1|1	1|1	0|1	1|1	0|1	0|1	0|1	0|0	0|0	0|1	0|1	1|1	0|1	1|0	1|1	1|0	1|0	1|0	0|0	1|1	1|0	1|1	1|0	1|1	1|1	1|1	1|1	1|1	0|0	1|1	0|1	0|1	1|1	1|1	1|0	1|1	1|1	0|1	1|1	1|1	1|1	1|1	1|0	1|1	0|1	0|0	1|1	1|0	1|1	1|1	1|1	1|1	1|1	1|0	1|0	1|1	0|1	0|1	1|1	1|0	1|0	1|0	0|0	0|1	1|0	0|1	1|1	0|0	1|0	1|0	0|1	1|1	1|1	1|1	1|1	1|0	1|1	1|1	1|0	0|1	1|1	0|1	0|1	0|1	0|0	1|1	0|1	1|1	0|1	0|1	1|1	0|1	

I have another file which contains the individual ID:

    head individual_id
        
    HG00096
    HG00097
    HG00099
    HG00100
    HG00101
    HG00102
    HG00103
    HG00105
    HG00106
    HG00107
    HG00108
    HG00109

the first individual in the ID file corresponds to the first genotype in the vcf file, and so on. For each position,I want to attach ID to each genotype and get an output and save the output in a seperate file like this :

    head desired_output_pos49444858
        HG00096      0|1
        HG00097      1|0
        HG00099      0|1
        HG00100      1|0
        HG00101      0|1

Does anyone have an idea how can I make this file?
Thanks

assuming that the number of lines in  individual_id is the same as the number of genotypes in the vcf...

 

       cat all_unique.vcf  | while read L ; do P=$(echo "$L" | cut -f2);paste <(cat individual_id ) <(echo "$L"| cut -f 10- | tr "\t" "\n" ) > "desired_output_pos${P}";done

