Question: How to apply vcftools --diff to identify vcf-specific variants/records
0
9 weeks ago
Shicheng Guo ♦ 7.5k

HI All,

Apply vcftools --diff, it is easy to find command/shared variants between two VCF files.

vcftools --vcf  A.vcf --diff B.vcf --diff-site 

However, Is there any easy to identify A specific or B specific variants?

Here is what I noticed:

Parameters as interpreted:
        --vcf gnomad.exomes.r2.1.sites.chr21.rec.ExomeStop.vcf
        --diff gnomad.exomes.r2.1.sites.chr21.rec.ExomeStop.vcf.vat
        --diff-site-discordance

After filtering, kept 0 out of 0 Individuals
First Header entry should be #CHROM: #OM
Outputting Discordance By Site...
Found 1696 sites common to both files.
Found 57 sites only in main file.
Found 0 sites only in second file.
After filtering, kept 1753 out of a possible 1753 Sites
Run Time = 0.00 seconds

I want to extract these 57 sites which only belong to main file (the first file) ...

Thanks.

Sorry. It looks I find the solution:

 awk '$3==1' out.diff.sites | wc -l
ADD COMMENTlink 10 weeks ago Shicheng Guo ♦ 7.5k • updated 9 weeks ago Istvan Albert 80k
0
9 weeks ago
Istvan Albert 80k
University Park, USA

Just testing

awk '$3==1' out.diff.sites | wc -l
ADD COMMENTlink 9 weeks ago Istvan Albert 80k
0

Yo RamRS

ADD REPLYlink 9 weeks ago
Istvan Albert
80k
0

Adding a user handle will trigger messages (and an email) depending on the user profile settings

@RamRS8494

will render as @RamRS8494

users may change their handle

ADD REPLYlink 9 weeks ago
Istvan Albert
80k
1

I was just getting here to do that, Istvan Albert!

(edited Istvan Albert####)

ADD REPLYlink 9 weeks ago
RamRS
21k • updated 9 weeks ago
Istvan Albert
80k
0

@<handle> followed by punctuation stops the handle from rendering as a username. Seems like the URL-followed-by-parentheses bug.

ADD REPLYlink 9 weeks ago
RamRS
21k
0

I thought we fixed that ... and we did but probably reintroduced it later on, very annoying

ADD REPLYlink 9 weeks ago
Istvan Albert
80k
0

Lets see what happens here https://www.reddit.com/

ADD REPLYlink 9 weeks ago
Istvan Albert
80k
0

Works fine. URL is no longer a problem, only handles are, Istvan Albert! ...

ADD REPLYlink 9 weeks ago
RamRS
21k • updated 9 weeks ago
Istvan Albert
80k
0

I wonder if parentheses are still lumped into urls (like http://www.google.com).

ADD REPLYlink 9 weeks ago
Devon Ryan
90k
0

That's been fixed, great!

ADD REPLYlink 9 weeks ago
Devon Ryan
90k

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