Edit IDs columns in vcf files by removing the ID first and then add new column

I have a vcf file. I need to update the ID column with this information.
This is how my vcf file looks like:

pic51891×931 55.1 KB

0797 NA20798 NA20799 NA20800 NA20801 NA20802 NA20803 NA20804 NA20805 NA20806 NA20807 NA20808 NA20809 NA20810 NA20811 NA20812 NA20813 NA20814 NA20815 NA20816 NA20819 NA20826 NA20828
chr22 16050408 . T C 100.00 PASS AA=.;AC=134;AF=0.06;AFR_AF=0.10;AMR_AF=0.05;AN=2184;ASN_AF=0.04;AVGPOST=0.9799;DAF_GLOBAL=.;ERATE=0.0046;EUR_AF=0.06;GERP=.;LDAF=0.0649;RSQ=0.8652;SNPSOURCE=LOWCOV;THETA=0.0149;VT=SNP;ANNOTATION_CLASS=ACTIVE_CHROM;CELL=GM12878;CHROM_STATE=13
GT:GL:DS:PP:BD .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.:. .:.:.:.

So, I want to update this site "." with chr22_16050408_T_C_b37 so each ID column in my vcf file should look like chr{no.}position_refallele_altallele_b37.

I tried to use the following command but its now giving me the answer.

awk 'NR>1 {print $1""$2""$3""$4"_b37"}' genotype_chr22_filtered_dosage1.txt

@rheab , hi,

• where is ID column in this ?

• show ACTUAL EXPECTED output required.

• use the MARKDOWN tags to display data not a stream of text that is hard to decipher please

• is that single awk line all you attempted ?

TEAM, please wait till @rheab has responded with their attempt(s) before assisting

I am able to remove the ID column using bcftools. Now I just need to update the ID column using the new format. I have editted my post.

@rheab , look at the response given in the link below.

However, we would appreciate if you can explain WHY this is being done (as we see a number of identical requests .... ).

This is either homework or multiple accounts asking the same question.