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help with vcftools filtering on individuals

Hi all, new to vcftools. I have a vcf file that I need to 1) filter via sample ID and 2) run frequency and LD analysis.

I have no problems with the --freq and --hap-r2 on the vcf file, however, I can't seem to get the filtering on sample ID to work?

I tried using a txt file with 950 sample IDs I want to keep:

vcftools --vcf AA_TAS2R38_HAPLO.vcf --freq --out AA_HAPLO_12M_freq --keep AA_12M.txt

VCFtools - 0.1.15
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf AA_TAS2R38_HAPLO.vcf
    --keep AA_12M.txt
    --freq
    --out AA_HAPLO_12M_freq

Keeping individuals in 'keep' list
After filtering, kept 1 out of 1305 Individuals
Outputting Frequency Statistics...
After filtering, kept 1 out of a possible 1 Sites
Run Time = 0.00 seconds

So I'm not sure what's happening? My "keep" file is just one sample name per line in a txt file. If I just use the --remove-indv it works just fine:

vcftools --vcf AA_TAS2R38_HAPLO.vcf --freq --out AA_HAPLO_12M_freq --remove-indv 4_1969-01D_02-013-1

VCFtools - 0.1.15
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf AA_TAS2R38_HAPLO.vcf
    --freq
    --out AA_HAPLO_12M_freq
    --remove-indv 4_1969-01D_02-013-1

Excluding individuals in 'exclude' list
After filtering, kept 1304 out of 1305 Individuals
Outputting Frequency Statistics...
After filtering, kept 1 out of a possible 1 Sites
Run Time = 0.00 seconds

This makes me think it is the format of my keep file? Or am I missing something in the header somewhere?

Thanks all!

NitDawg

vcftools
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updated by pduluth96 • pduluth96 • written by schisler • schisler

I can't be sure but it could be due to the end-line character in your keep text file. In which editor and operating system did you create it?

In the past, I have had issues with text files created in Windows that I then transported to linux. There's a very simple program called dos2unix that could assist. Here it is for ubuntu: https://launchpad.net/ubuntu/trusty/+package/dos2unix

Also check those hypens in your keep file and be sure that they are exactly the same as in the VCF. I have also had issues time and time again with different types of hyphens - there are various in the ASCII encoding.

• 0 views • link
written by Kevin Blighe Kevin Blighe

Yup! That was it, the encoding.

This is on an OSX machine using TextMate. The default was Unicode - UTF-8. I switched to Western - Windows and viola.

Thanks a ton. I banged my head for an afternoon.

• 0 views • link
written by schisler • schisler

No problem. Yes, you wouldn't believe how much this issue frustrated me the first time that I encountered it. I think that it was back in 2014.

Good luck! Kevin

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written by Kevin Blighe Kevin Blighe

Not all hyphens are created equal apparently. Filed away in the tip jar. Cheers Kevin.

• 0 views • link
written by schisler • schisler

1 answer

For anyone that has a similar problem ( I had it reversed: keep worked, but remove-indv didn't), remember that you can just give the name of the individual you want to keep / exclude, instead of giving a text file containing its name: e.g.

vcftools --gzvcf my_vcf.vcf.gz --remove-indv S12794  --recode

EDIT: apparently this only works with --remove-indv, not with --keep.

• 0 views • link
written by pduluth96 • pduluth96

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