[laura]

What aspects of the format are you struggling with

The genotypes are shows as index values on the Ref/Alt columns so in your case T is 0 and C is 1

This gives you your give genotypes for this site being T/C, C/C, C/C, T/C, T/C, T/C

[aforntacc]

What aspects of the format are you struggling with

The genotypes are shows as index values on the Ref/Alt columns so in your case T is 0 and C is 1

This gives you your give genotypes for this site being T/C, C/C, C/C, T/C, T/C, T/C

Ok, thank you very much, at first i was reluctant to analyse this part of the data but when i saw the previous threads on this website i was encouraged so thanks once again.

Please what use are these (AltSup AC1=12;AF1=1;DP4=0,0,1,1;DP=66;FQ=-26.9;MQ=39;MfGt=0/1;MinDP=0;NeqMfGt=2) for my analysis since i am only interested on the SNPs and INDELS that pass the filtering criteria and their differences among my libararies and not the Reference.
secondly the way you interpreted the GT index is it ture for all sites that pass the quality craiteria.
thank you

[laura]

Those fields will be determined by what ever analysis package you used to generate your vcf file

Some of them might be standard fields which are all explained in the VCF documentation

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

[aforntacc]

Those fields will be determined by what ever analysis package you used to generate your vcf file

Some of them might be standard fields which are all explained in the VCF documentation
http://www.1000genomes.org/wiki/Anal...mat-version-41

thanks a lot laura
i am only interested in the difference among the wt and mt, from which i will select candidate regions. i am more than happy if you can point me towards the right direction, this is my very first time handling this kind of data.
thanks

[laura]

If you want to know the difference between your WT and MT individuals you need to compare their genotypes

[aforntacc]

Thank you Laura, gradually i am making progress.
please i want to ask but i dont know if this is a stupid question
if i want to uncode the GT index for all SNPs that pass the filter criteria how can i do that?
specifically do i have to do this with the VCF tools (decode genotype) using the PERL5LIB environment or what? am a bit confused please.
thanks a lot

[laura]

Unfortunately that is a bit of a how long is a piece of string question as it very much depends on what tools/programming language you wish to use to do it

If you want a vcf file with just PASS snps in it you can use the vcftools binary and its --remove-filtered-geno-all option but if you want other info than that then it depends

[aforntacc]

hi laura
i am still progressing small small
but i have got this error when i want to output the vcf file with passed snps ( --remove-filtered-geno-all)
bilbo@ubuntu:~/vcftools_0.1.4a$ ./cpp/vcftools --vcf /media/My\ Passport/other\ analysis\ by\ fasteris/2012-02-21_GQJ-1-6_VitisVinifera_variants.vcf --remove-filtered-geno-all --out /media/My\ Passport/other\ analysis\ by\ fasteris/lagolas.vcf

VCFtools - v0.1.4
(C) Adam Auton 2009

Parameters as interpreted:
--out /media/My Passport/other analysis by fasteris/lagolas.vcf
--remove-filtered-geno-all
--vcf /media/My Passport/other analysis by fasteris/2012-02-21_GQJ-1-6_VitisVinifera_variants.vcf

Scanning /media/My Passport/other analysis by fasteris/2012-02-21_GQJ-1-6_VitisVinifera_variants.vcf ...
Error:VCF version must be v4.0:
You are using version VCFv4.1

now i am stuck, please what should i do.
thanks

[laura]

It looks like you either need to investigate if your problem can be solved with the vcftools perl scripts or maybe change your header from vcf4.1 to vcf4.0 and see what the vcftools binary does

These questions are now most appropriate for the vcftools-help list which you can find

http://vcftools.sourceforge.net/

[aforntacc]

Hi all

i dont have snp id in my data, the ID column is all in dot (.) why is this because i am able to filter out the indels but not the snps
how can i do this.
thanks
#CHROM POS ID REF ALT
chr1 8686 . T C
chr1 10802 . T C
chr1 10815 . A G
chr1 10836 . C A
chr1 11355 . C A
chr1 11433 . T C
chr1 11669 . ATTTT ATTTTT

[laura]

The missing ids are unlikely to be the cause of this

You need to provide specific details about the filtering methods you are choosing if people are going to help figure out what is wrong

[aforntacc]

Hello

Please i want to find out how i can interpret the indels, i have some thing like this chr3 4466963 . TGGAG TGGAGGAG 999 PASS AC1=5;AF1=0.4167;DP4=7,197,3,84;DP=347;FQ=999;G3=0.1667,0.8333,8.319e-50;HWE=0.0465;INDEL;MQ=44;MfGt=0/1;MinDP=28;NeqMfGt=1;PV4=1,1.5e-70,2e-112,1 GT:PL: DP:SP:GQ 0/1:93,0,255:33:0:95 0/0:0,122,255:59:0:99 0/1:53,0,241:42:0:55 0/1:139,0,250:59:7:99 0/1:78,0,255:70:3:80 0/1:62,0,238:28:0:64
so will it be like this TGGAG = 0 and TGGAGGAG = 1 as the same for the snps. or is it interpreted differently?
secondly how can i use the vcftols to compare two individuals (i have seperated them into two vcf files) with 3 libraries WT (0/1:93,0,255:33:0:95 0/0:0,122,255:59:0:99 0/1:53,0,241:42:0:55) and
MT (0/1:139,0,250:59:7:99 0/1:78,0,255:70:3:80 0/1:62,0,238:28:0:64).
thanks a lot

[aforntacc]

Please i want to find out how i can interpret the indels, i have some thing like this chr3 4466963 . TGGAG TGGAGGAG 999 PASS AC1=5;AF1=0.4167;DP4=7,197,3,84;DP=347;FQ=999;G3=0.1667,0.8333,8.319e-50;HWE=0.0465;INDEL;MQ=44;MfGt=0/1;MinDP=28;NeqMfGt=1;PV4=1,1.5e-70,2e-112,1 GT:PL: DP:SP:GQ 0/1:93,0,255:33:0:95 0/0:0,122,255:59:0:99 0/1:53,0,241:42:0:55 0/1:139,0,250:59:7:99 0/1:78,0,255:70:3:80 0/1:62,0,238:28:0:64
so will it be like this TGGAG = 0 and TGGAGGAG = 1 as the same for the snps. or is it interpreted differently?
secondly how can i use the vcftols to compare two individuals (i have seperated them into two vcf files) with 3 libraries WT (0/1:93,0,255:33:0:95 0/0:0,122,255:59:0:99 0/1:53,0,241:42:0:55) and
MT (0/1:139,0,250:59:7:99 0/1:78,0,255:70:3:80 0/1:62,0,238:28:0:64).
thanks a lot[/QUOTE]

[laura]

You may find it more fruitful to start another post with this question with a more specific title

How do you interpret a particular indel is really a how long is a piece of string question, what are you trying to find out, what hypothesis are you testing and these will determine how you might look at your result

vcf tools has various scripts to produce intersections and compare two different vcf files, which tools are appropriate again very much depends on what questions you want to answer

I would think about the specific questions you wish to answer and come back with a new thread and more information and you may get more help that way

[aforntacc]

OK, i have opened a new thread,
i have only one objective to compare wt (0/1:93,0,255:33:0:95, 0/0:0,122,255:59:0:99 0/1:53,0,241:42:0:55) and mutant (0/1:139,0,250:59:7:99, 0/1:78,0,255:70:3:80 0/1:62,0,238:28:0:64).
to find what is common indels and unique ones
and i kindly ask please do i interpret the indels as the way the snps are interpreted. as in ref =0 alt =1. because i tried to read stuff about indels i cant find anything useful so i turn to this site for the much need help.
thanks a lot for your help i am grateful