Automatize extraction of a VCF column value

Question

[jomagrax]

I need to automatize a command line software (pvacseq tools) where I need the 12th column of the row that contains "CHROM" of each file to be a parameter, this is what I have thought:

for i in *.vcf  ; do  pvacseq run \ 
$i \ 
awk'/CHROM/{print $12}' ${i}\ 
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \ 
"${i%%_vep*}_pvac-result"   ; done

The problem seems that with each space of the awk command, pvacseq unserstands that a new option It's been introduced.

So I guess what I need is a way of automatizing the extraction of that column in a single command without spaces or a way for the program to understand that the awk command is a single command even thought if It has spaces.

About the replication of the problem I don't know how to approach It since installing pvaseq can be complicated.

Answer 1

[jomagrax]

I found the solution

for i in *.vcf
do
    x=$(awk '/CHROM/{print $12}' ${i})
    pvacseq run $i $x HLA-A*02:01,HLA-B*35:01,DRB1*11:01 ... 
    #              ^^
done

Answer 2

[Pierre Lindenbaum]

I'm not sure I understand your problem instead of awk'/CHROM/{print $12}' ${i}\

may be you just want:

$( bcftools query -l "${i}" | awk '(NR==3)')

using a command substitution https://www.gnu.org/software/bash/manual/html_node/Command-Substitution.html