1000 genomes VCF format?

[yuanzhi]

I am trying to figure out the SNP genotype from the 1000 genomes VCF format

#CHROM POS     ID        REF ALT    QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
20     14370   rs6054257 G      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20     17330   .         T      A       3    q10    NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3   0/0:41:3
20     1110696 rs6040355 A      G,T     67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2   2/2:35:4

Is the SNP genotype just the column of "ALT"?

Thanks

[quinlana]

There should be two files: one with the sites of polymorphism (the one you show here) and another with the genotypes at said sites. Look for *.genotypes.* or something like that.

[yuanzhi]

Hi, Quinlana

Thanks for your answer! I am trying to figure out if I used the wrong term. When I said "SNP genotype", I meant "SNP call". For example, if the reference is A/A and the SNP call is T/T, "T/T" is the "SNP genotype" that I am looking for.

Your "genotype" is the genotyping SNP call (not the sequencing SNP call), right?

I apologize for my lack of knowledge of these terms. I have been trying to look for a book or something like that which can tell me the correct definition of SNP call, SNP genotype, base call, polymorphisms, and etc.

Thanks again

[Jose Blanca]

You have plenty of information about the format at the 1000genomes vcf page.

[laura]

The ALT column defines the possible alternative alleles, columns 10->n define a specific individuals genotype

[laura]

As an update there 1000genomes website has recently changed its backend and therefore url structure

The spec can now be found

http://www.1000genomes.org/wiki/Analysis/Variant Call Format/vcf-variant-call-format-version-40

[johnadam33]

I am new to this field and I am trying to figure out how t use this data in vcf format from myself. I am looking to open these files so that I can look for some SNPs at a given location. Do u all know how to access the wiki page. Do we need to login and so how to register?

[laura]

http://www.1000genomes.org/wiki/Analysis/Variant Call Format/vcf-variant-call-format-version-40

These are public pages within the wiki

you shouldn't need to log in to see the

Most of the 1000 genomes wiki is a internal project tracking wiki so logins are not provided to people outside the project

[johnadam33]

Thanks a lot Laura. That helps. I guess I have to do some ground work in order to access them.

[johnadam33]

Very Urgent and IMP

Can anyone tell me why the human ref sequence is diff in 1000 genome browser when compared to sequence at NCBI,Ensembl, and USCS browsers. I am looking at variant call data, the chr seq location has different base in 1000 genome browser than other three (all same).
Thanks,

[laura]

The pilot analysis for 1000 genomes was done using the NCBI36 assembly but the browsers are all now using the GRCh37 assembly which leads to different coordinates

The 1000 genomes main project uses GRCh37 and there are snps available from the ftp site for these but the browser has yet to be updated

[johnadam33]

Thanks for the reply Lauara.
So how much difference is there? If I want to see for a location say chr1:10041132 (on GRCh37) with that of ncbi36 build, what should I do?

[laura]

For variants it is safest to use rs numbers which dbSNP track from one assembly to another.

To map specific positions though ensembl provides a tool

http://www.ensembl.org/tools.html

[vyellapa]

Im looking for a link of genotypes vcf of the latest 1000 genome release and the corresponding reference. I can see one at the link below but it seems to the older release (629 individuals and vcf 4.0). Can I know where I can find the same file in the newer release.

ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz

Thank you,
Teja

[laura]

The final call set for Phase 1 (1092 individuals) you can find here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1...ted_call_sets/

Please have a look at the README:

ftp://ftp.1000genomes.ebi.ac.uk/vol1...l_set_20120621

All calls are relative to the GRCh37 / hg19 genome assembly.