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Question: Remove variants from VCF by INFO tag
0
gravatar for bioroma.spb
4.8 years ago by
bioroma.spb • 50
Saint-Petersburg, Russian Empire
bioroma.spb • 50 wrote:

Hello everyone,

I have a whole folder of VCF's generated by GATK CombineVariants. I want to remove variants (entire rows) containing ":R" or ":F" (but not ":FR") strings in INFO column. What is the best way to do this?
awk gatk vcf • 1.6k views
ADD COMMENT • link •
modified 4.8 years ago by Matt Miossec • 350 • written 4.8 years ago by bioroma.spb • 50
3
gravatar for Matt Miossec
4.8 years ago by
Matt Miossec • 350
UK/Oxford/Wellcome Centre for human genetics
Matt Miossec • 350 wrote:

You could use a simple AWK command (assuming the INFO column is the 8th column):

`awk '$8!~/:R/ && $8!~/:F[^R]*$/` FILE.vcf > FILE_updated.vcf

Removes all lines with either :R or :F (unless :FR)

If you want to do it for all your VCF files:

for file in `ls *.vcf`; do **awk command above** $file > ${file%%.vcf}_updated.vcf ; done

Iterates through all the .vcf files in your current directory.
ADD COMMENT • link modified 4.8 years ago • written 4.8 years ago by Matt Miossec • 350
1

Thank you! Problem solved.

ADD REPLY • link written 4.8 years ago by bioroma.spb • 50
1

UPD: I've encountered another problem: command you wrote leaves rows with :F at the end of the column. Do you have any suggestions why?

ADD REPLY • link written 4.8 years ago by bioroma.spb • 50
1

I've updated the AWK command to take that into account. The awk commands interprets '[^R]' as "any term that isn't R". So if ':F' is at the end of the field, it will not exclude it because it is expecting a term that isn't there. I have fixed this issue by writing '[^R]*$' instead. The asterix stands for "0 or more" and the dollar sign stands for the end of the field. It will therefore remove lines with ':F' if it's at the end of the field or otherwise anything that isn't ':FR'.

ADD REPLY • link written 4.8 years ago by Matt Miossec • 350
1

Thank you again! Now everything works well.

ADD REPLY • link written 4.8 years ago by bioroma.spb • 50
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