bcftools query add header

Question

[User000]

Hello,

I have a vcf file and I extract only some columns like FILTER, and GT and DP values.

bcftools query -f '%FILTER[\t%GT\t%DP]\n' {input} > {output}

This gives me an output without a header, is it possible to add a tab delimited header like FILTER GT DP?

    FILTER GT DP
    PASS 1/1 89
    PASS 0/1 78

Answer 1

[User000]

I found an easier way:

bcftools query -H -f '%FILTER[\t%GT\t%DP]\n' {output} -o {output}

[jon.klonowski]

Should be

bcftools query -H -f '%FILTER[\t%GT\t%DP]\n' {input} -o {outputname}

This includes header but, for me, also numbers before the names:

#[1]FILTER [2]GT [3]DP

Answer 2

[Pierre Lindenbaum]

(bcftools query -l in.vcf | awk 'BEGIN{printf("FILTER");} {printf("\t%s_GT\t%s_DP",$1,$1);} END{printf("\n");}'  &&  bcftools query -f '%FILTER[\t%GT\t%DP]\n' in.vcf ) > out.tsv

[User000]

thanks a lot, this gives me an error:

IndexError: list index out of range
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 140, in run_jobs
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 441, in run
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 230, in _run
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 156, in _run
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 162, in printjob

[Pierre Lindenbaum]

I'ts unrelated to your original problem. Looks like a snakemake error. See if awk statements need to be escaped.

[User000]

NameError: The name 'printf("FILTER");' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}}
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 140, in run_jobs
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 441, in run
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 230, in _run
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 156, in _run
  File "/usr/local/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 162, in printjob

[Pierre Lindenbaum]

at this point I stop helping you.

[User000]

it says syntax error at END{printf... but I dont know how to solve this since I do not understand what exaactly the code does without any explanations.

Answer 3

[DBScan]

In case somebody else stumbles upon this question, -HH disables the column numbers:

 bcftools query -HH -f '%CHROM\t%POS\t%REF\t%ALT\n' input.vcf

Output will be

#CHROM  POS     REF     ALT
chr1    10000   A       T
chr1    20000   G       C
chr1    30000   T       A