vcftools-help — Mailing list for help using VCFtools

[Vcftools-help] Extraction of SNPs

[Volodymyr D. <vdv...@al...>]

Hello,

I searched the forum but have not found an answer to my question which is the following:

Is it possible to extract the genotypes of specific SNPs in a single file, which contained the information about the individuals, their genotypes, and respective populations (super- and subpopulations)? Could you kindly provide a command line for this operation?

Thank you,

Volodymyr





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[Vcftools-help] Please help to resolve compatibility issues.

[stalin.shaji . <sta...@ca...>]

Hi sourceforge team, 
I would like to install vcftools_0.1.12a version which is old. Could you please provide corresponding CPP and Perl version compatible to this vcftools version. Please mention any other requirements for successful installation.
I am currently facing error during installation, when executing 'make' inside vcftools Dir. 

Thank you
Stalin Dany

[Vcftools-help] Vcftools fst statistics

[Lukas C. <luk...@gm...>]

Hello,

My name is Lukas Chumchal and I have a problem with vcftools fst statistics
format.

I used on my vcf file same command as mentioned in documents. I separate my
vcftools samples (95) according to relation to case control study from I
have my data - 63 samples as first population - Case; from 64 to 95 -
Control. I am using windows 10 and using vcftools with WSL-2.

Unfortunately I noticed, that after I open .fst results with Notepad++ I
got only 69599 values from 78587 rows of vcf file. In log file there is no
problems and it said 78587 keeps 78587.

I don't know what to do. I tried to use unix2dos before opening the file,
check encryption, but nothing changed.

Maybe it can be problem with missing values in vcf file. It there any way
how to prevent this data lost? Can this be solved with somehow manipulating
the possible missing values?

I am so sorry If I am not clear enough, but right now I am desperate.

Sincerely

L.Ch

[Vcftools-help] Keep other columns before INFO when use --get-INFO

[Quanwei Z. <qwz...@gm...>]

Hello:

We have vcf file in format like below. We used "vcftools --vcf ${input_vcf}
--get-INFO CLASS --get-INFO GENE --get-INFO DNA --get-INFO PROT --get-INFO
PHEN --out ${output_file_step1}" to extract some features. But the result
also filter out "ID", "QUAL", "FILTER" column (example as picture below).
How can I keep those columns in the output?

#the input vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       865595  CM1613956       A       G       .       .
CLASS=DM?;MUT=ALT;GENE=SAMD11;STRAND=+;DNA=NM_152486.4%3Ac.133A>G;PROT=NP_689699.3%3Ap.K45E;DB=rs903331232;PHEN="Retinitis_pigmentosa";RANKSCORE=0.21

#result
[image: image.png]

Thanks

Best
Quanwei

[Vcftools-help] remove samples from vcf

[Torres L. J. <jav...@ku...>]

Hello.

I’m trying to remove specific samples (columns) from my vcf file. I’m using the manual syntax, which generates an output file but it's corrupted.

vcftools --remove-indv sample_name --vcf my.vcf --out my_filtered.vcf

Also, I need to remove several samples and I’m not sure if I have to do it one by one or there’s a way of doing batches.

I’d appreciate any help.

[Vcftools-help] --het F reference?

[Mark M. (EI) <Mar...@ea...>]

Hi,

I’m using the inbreeding coefficient F and I wondered if anyone knows reference for the calculation of F?  I have negative F values which I guess from other inbreeding coefficient literature suggests an excess of heterozygous loci.  However, it would be good to have the source to confirm.

Best,
Mark

Dr Mark McMullan
Evolutionary Biologist
[signature_1739357713]<http://www.earlham.ac.uk/>
mar...@ea...<mailto:mar...@ea...>
mcm...@gm...<mailto:mcm...@gm...>
[signature_776859034]<http://www.earlham.ac.uk/mark-mcmullan>|[signature_1002920702]<https://twitter.com/mcmullan0>|[signature_739174286]<https://scholar.google.co.uk/citations?user=Ka-91IAAAAAJ&hl=en>

[Vcftools-help] VCF tools Hardy weignberg option

[Damayanti, N. P <nda...@iu...>]

Dear VCFtools team.

I tried to get p Value for each of my SNP from my bcf file, with this

 vcftools --bcf ht128a.bcf --hardy  --max-missing 1.0 --out outputh128_noMissing

but I always received this message:

After filtering, kept 1 out of 1 Individuals
Outputting HWE statistics (but only for biallelic loci)
After filtering, kept 0 out of a possible 0 Sites
File does not contain any sites
Run Time = 1.00 seconds


what did I do wrong? thank you

Nuri

[Vcftools-help] [SPAM] screw airend

[Carrie c. <sa...@cn...>]

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[Vcftools-help] (no subject)

[robert k. <rob...@se...>]

Vcftools
 
 
https://j.mp/38QQBVg
 
 
robert king
 

[Vcftools-help] The use permit of Vcftools

[Quanshun M. <au6...@un...>]

Dear Authos,

I'm a phD student in animal breeding. Vcftools is a very useful software in genotype data analysis, for convenience,  i develop a R package to interact with  software Vcftools. In order to facilitate the analysis procedure, i want to predownload  software- Vcftools in this R package, is it legal? Of course, this package would show the related messages that lets people know  this function is achieved by Vcftools. Thank you!

Best regards
Quanshun

[Vcftools-help] Help: report all variants?

[Bradley, C. C. <Cat...@bc...>]

Hello,

I'm looking for a way to split multiple variants reported at a single position into separate lines (1 var per line), while also keeping all variants, even redundant ones. Your vcfbreakmulti tool almost did it for me, but I noticed it only split the unique variants at each position and dropped the repeats.

Thanks for your help!

-Cathy

[Vcftools-help] How do you do?

[robert k. <rob...@bo...>]

Vcftools
 
https://bit.ly/3w7ybcg
 
 
 
 
 
robert king

[Vcftools-help] How does --weir-fst-pop handle multiallelic sites?

[Alyssa L. F. <afo...@st...>]

Hello!

How does --weir-fst-pop handle multiallelic sites? From the Weir and Cockerham (1984) paper, I see that their recommendation for an unbiased combined estimate over multiple alleles at the same site is:
thetaw = sumu(au) / sumu(au+bu+cu)
where w is a site and u are all the different alleles at the site.

I just wanted to confirm that this is how vcftools is handling multiallelic sites... let me know if you know!

Thanks!
Alyssa Lyn Fortier
PhD Candidate, Stanford University
Jonathan Pritchard Lab

[Vcftools-help] Interpreting .imiss file from vcftools

[Torres L. J. <jav...@ku...>]

Hi everybody,

I’m following the pipeline of Cerca et al. (2021) to identify missing data from vcf files.

I ran vcftools with the --missing-indv flag. The output is an .imiss file with the following columns: INDV, N_DATA, N_GENOTYPES_FILTERED, N_MISS, F_MISS.

Could anyone explain what information we get from N_DATA, N_MISS, F_MISS?

From the supplementary data from Cerca el al. (2021) it seems that N_MISS, F_MISS are “number of missing sites” and “percentage of missing sites” respectively but I’m not entirely sure.

Thanks for the help.

[Vcftools-help] [SPAM] Greetings vcftools help!

[robert k. <rob...@dc...>]

  Vcftools        https://bit.ly/3fST2tA        

robert king

[Vcftools-help] Ethiopian American Civic Council (EACC): Ethiopia will never surrender its sovereign right / ክብርና ሉዓላዊነታችንን

[<dms...@gm...>]

Hey,

I just signed the petition "Ethiopian American Civic Council (EACC):
Ethiopia will never surrender its sovereign right / ክብርና ሉዓላዊነታችንን" and
wanted to see if you could help by adding your name.

Our goal is to reach 5,000 signatures and we need more support. You can
read more and sign the petition here:

http://chng.it/Wz8njZ7Rmx

Thanks!
Demissew Sertse

Re: [Vcftools-help] Help

[shazia k. <kun...@gm...>]

Hi,

Please check this link given below.

https://anaconda.org/bioconda/vcftools

You can run this command on your server terminal.

I hope it will work for you.

On Sat, 8 May 2021 at 17:58, simran.singh.sengar3 <
sim...@gm...> wrote:

> use Ubuntu system in Linux. that's super easy
>
>
>
> sim...@gm...
> Sent from my realme phone
> On danieliyaah <dan...@16...>, 8 May 2021 20:53 wrote:
>
> Hello,
> Please am new in Linux system however I am working on GWAS and I need to
> install vcftools and plink in our Linux server for the onward analysis. Am
> using SHH secure shell
> Please can you help me ?
>
> Thank you
>
> Daniel
>
> Student of China Agricultural University
>
>
>
>
> _______________________________________________
> Vcftools-help mailing list
> Vcf...@li...
> https://lists.sourceforge.net/lists/listinfo/vcftools-help
>


-- 
Best regards,
Shazia Kunvar

Re: [Vcftools-help] Help

[simran.singh.sengar3 <sim...@gm...>]

<div dir="ltr">use Ubuntu system in Linux. that&#39;s super easy<br>
</div><div dir="ltr"><br>
</div><div dir="ltr"><br>
</div><div dir="ltr"><br>
</div><div class="max-body" style="width: 100%; border-radius: 5px; overflow: hidden; max-width: 360px; margin-left: 0;"><div class="max" style="width: 100%; margin: 0 auto; max-width: 360px; margin-left: 0;"><table border="0" cellpadding="0" cellspacing="0" style="width:100%;"><tr style="vertical-align:top;"><td style="background: #ffffff; background-position: center center; background-repeat: no-repeat; padding: 0; vertical-align: top; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;" height="0" valign="top"><div class="mj-hero-content" style="margin:0px auto;"><table border="0" cellpadding="0" cellspacing="0" style="width:100%;margin:0px;"><tr><td style="font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;"><table border="0" cellpadding="0" cellspacing="0" style="width:100%;margin:0px;"><tr><td align="left" class="container theme" style="background: #F0F0F0; background-image: linear-gradient(-45deg, #F0F0F0 0%, #FAFAFA 100%); font-size: 0px; padding: 24px 15px 14px; word-break: break-word; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana; margin-left: 0;"><table cellpadding="0" cellspacing="0" width="100%" border="0" style="color:#000000;font-family:Ubuntu, Helvetica, Arial, sans-serif;font-size:13px;line-height:22px;table-layout:auto;width:100%;border:none;"><tr><td class="reset-font h-22" style="font-size: 0; min-height: 22px; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;"><div class="font-16 fw-600 pr-20" style="font-weight: 600; font-size: 16px; padding-right: 20px;"><span class="mr-5" style="margin-right: 5px;"></span> <span class="font-10 fw-400" style="font-weight: 400; font-size: 10px;"></span></div></td><th valign="top" rowspan="2" class="avatar reset-font" style="font-size: 0; 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height: 42px; border-radius: 8px; border: 0;" width="42" height="42"></th></tr><tr><td class="normal-text font-14 h-16 lh-16" style="font-size: 14px; line-height: 16px; height: 16px; word-wrap: break-word; word-break: break-all; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;" height="16">simran<span>.</span>singh<span>.</span>sengar3<span>@</span>gmail<span>.</span>com</td></tr><tr><td colspan="2" class="h-23 reset-font" style="font-size: 0; height: 23px; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;" height="23"></td></tr><tr><td colspan="2" class="normal-text lh-16 font-12" style="font-size: 12px; line-height: 16px; word-wrap: break-word; word-break: break-all; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;"></td></tr><tr><td colspan="2" class="normal-text lh-16 font-12" style="font-size: 12px; line-height: 16px; word-wrap: break-word; word-break: break-all; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;"></td></tr><tr><td colspan="2" class="normal-text lh-16 font-12" style="font-size: 12px; line-height: 16px; word-wrap: break-word; word-break: break-all; font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;"></td></tr><tr><td colspan="2" class="footer font-10 lh-19" style="font-size: 10px; line-height: 19px; color: rgba(0, 0, 0, 0.5); font-family: &#39;PingFang SC&#39;, &#39;Hiragino Sans GB&#39;,&#39;WenQuanYi Micro Hei&#39;, &#39;Microsoft Yahei&#39;, &#39;微软雅黑&#39;, verdana;">Sent from my realme phone</td></tr></table></td></tr></table></td></tr></table></div></td></tr></table></div></div><div class="wps_quotion">On danieliyaah &lt;dan...@16...&gt;, 8 May 2021 20:53 wrote:<br type="attribution"><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p></p><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">Hello,<br>Please am new in Linux system however I am working on GWAS and I need to install vcftools and plink in our Linux server for the onward analysis. Am using SHH secure shell<br><div>Please can you help me ?</div><div><br></div><div>Thank you</div><div><br></div><div>Daniel</div><div><br></div><div>Student of China Agricultural University</div></div><br><br><span title="neteasefooter"><p> </p></span></blockquote></div>

[Vcftools-help] Help

[danieliyaah <dan...@16...>]

Hello,
Please am new in Linux system however I am working on GWAS and I need to install vcftools and plink in our Linux server for the onward analysis. Am using SHH secure shell

Please can you help me ?


Thank you


Daniel


Student of China Agricultural University

[Vcftools-help] Regarding estimation of Tajima's D by using VCFTOOLS

[Dr. D. R. <sim...@gm...>]

Sir, I am not able to put command for step size in vcftools please help me
out

[Vcftools-help] regarding estimation of Tajima's D

[divya r. <sim...@gm...>]

sir, i am not able to put command for step size in estimation of 
Tajima's D . please help out

[Vcftools-help] can't install vcftools

[李梓榕 <liz...@16...>]

when I want install vcftools,will have this error:
Unescaped left brace in regex is illegal here in regex; marked by <-- HERE in m/\${ <-- HERE ([^ \t=:+{}]+)}/ at /usr/bin/automake line 3935.
autoreconf: automake failed with exit status: 255

[Vcftools-help] seeking for help in installing vcftools

[啊 <sun...@12...>]

Dear developers of VCFTOOLS
  RecentlyI  tried to install VCFTOOLS under ubuntu environment, and I tried to build from release tarball following README.md. However, when I typed the command "./configure", it showed "bash: ./configure: No such file or directory". Is there something I did incorrectly? I would appericiate it if any developer support me to installing the software.
Thanks anyway
best regards.
sun

[Vcftools-help] [SPAM] VFD/Solar pump inverter/OFF Grid Inverter

[Sendadrive <in...@se...>]

Dear my friend,
Glad to know that you are focusing on automation and solar energy field. We are manufacturer of Hybrid Inverter with MPPT Controller/OFF Grid inverter/Solar pump inverter/Frequency inverter/VFD
Any interested please let me know. If you don't like to receive promotion email please let us know.We will never send you. Thank you!
-----------------------------------Best Regards
Liugang YU Sales Manager 
Shenzhen Senda drive technology Co.,Ltdwww.sendadrive.com Email: in...@se.../Whatsapp/Wechat/Skype: +86-18026904696

[Vcftools-help] Variant filtering options

[Baiba A. <bai...@gm...>]

Hello,
I need to filter my variants according to following criteria:
Qual > 30, FisherStrand (FS) < 60, RMSMappingQuality (MQ) > 40, Quality of
Depth (QD) > 2.0, StrandOddsRatio (SOR) <= 3.0, Genotype (GT) = 1, Genotype
quality (GQ) > 20, Total depth (DP) > 10 x and ALT Allele Depth (AD) >=
90%.

It is not clear, which filtering option is suitable for:  FisherStrand (FS)
and  StrandOddsRatio (SOR) - because I only found one option for filtering
strand bias;
Also I did not found options for Quality of Depth (QD) , Genotype (GT) = 1,
Genotype quality (GQ) > 20, and ALT Allele Depth (AD) in the manual
Do these commands even exist in VCFTools?


-- 
best regards,
Baiba Alkšere

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