No vcf output from vcftools

Question

[axelwilhelm]

I thought this command would give me a new vcf file without the individuals in the text file:

vcftools --gzvcf mergedPF.vcf.gz --remove listPnsToRemoveFromMergedVcf.txt --out filtMergedPTrios

Instead it gives me an index file and a log file.

I must be missing some obvious point. I want to filter out some individuals from the gvcf file for a new gvcf file. What is the fastest way of doing this? Like vcf-subset?

Edit:

adding --recode fixed it but the info field is gone.

vcf-subset -c pnsToKeepInCpTrio.txt copyPhasedCpTrio.vcf.gz > keptPnsFromCpTrio.vcf

worked also retaining info.

[Ram]

Just looked up the manual again, --recode-INFO or --recode-INFO-all might help you. I sure hope you're giving the manual a go before posting a question or reporting an issue.

[axelwilhelm]

I did, back and forth, missed the obvious and posted here. Sometimes people get dyslexic for what they are searching for. Like having the glasses on the eyebrows while searching for them.

[Ram]

No worries, as long as you checked the manual. It so happens at times that people just don't care enough to try and solve their problems by themselves before seeking help. I have done it a few times myself way back when.

Anyway. we're here to help you, in more ways than one!

Answer 1

[Ram]

Hi,

vcftools looks at the --recode option to re-write a VCF file. This change should work for you:

vcftools --gzvcf mergedPF.vcf.gz --remove listPnsToRemoveFromMergedVcf.txt --out filtMergedPTrios --recode filtMergedPTrios

Source: http://vcftools.sourceforge.net/man_latest.html#OUTPUT%20OPTIONS