Extracting Info From A Column Of Vcf File?

Question

[bioinfo]

I used the command below to get column 2,6 and 8 of my vcf file

cut -f 2,6,8 my.vcf  > out.vcf

output:

12 AA DP=23;AC=4;DC=5
13 BB DP=24;AC=6;DC=9
14 CC DP=34;AC=6;DC=65

For for INFO column (column 8), I want to get just DP from a list of things in that column (INFO column contains e,g. AN=2;DP=87;DC=56;Dels=0.00..)

What else should I add to that command? it will be great if I get all output in csv format.

Answer 1

[Random]

Normally I would also use awk, but in this case I think the use of VCFtools is warranted.

You can specify which fields and/or sub-fields you want to retrieve, as well as the separator in the output file.

In your case I would just use the VCFtools perl modules, and do vcf-query -f '%POS,%QUAL,%INFO/DP\n' my.vcf > out.vcf

[mg]

If using bcftools, here is equivalent command: bcftools query -f '%POS,%QUAL,%INFO/DP\n' my.vcf > out.vcf

Answer 2

[Pierre Lindenbaum]

Using my tool extractinfo: https://code.google.com/p/variationtoolkit/wiki/ExtractInfo

extractinfo -t DP  < my.vcf |   cut -f ' ' -1,2,12

[Pierre Lindenbaum]

this tool is deprecated. Use bioalcidae http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

Answer 3

[tommy.carstensen]

If your out.vcf is:

12 AA DP=23;AC=4;DC=5
13 BB DP=24;AC=6;DC=9
14 CC DP=34;AC=6;DC=65

simply do:

cut -f 2,6,8 my.vcf | awk -F \; '{print $1}' > out.vcf

[bioinfo]

the output looks like that:

DP=23

DP =24

DP=34

I want just numbers means

23

24

34

I also want the two other columns at the same output. So I was expecting something like that:

12 AA 23

13 BB 24

14 CC 34

[Istvan Albert]

then modify the script to become

cut -f 2,6,8 my.vcf | awk  '{OFS="\t";  split($3,x,";"); split(x[1],y,"="); print $1,$2, y[2]}'

generates:

12  AA  23
13  BB  24
14  CC  34

[bioinfo]

it worked...thanks

by the way when we do the 'editing of commands' how should we put that in a box like you did?

[Istvan Albert]

I think it makes it easier to read - just add four spaces at the beginning of a line to format it as code