Error loading vcf from gatk into Plink error

[Thomas Hartwig]

Hi,

I want to import a vcf file which I created using GATK via 34 gvcf files merged using gvcf genotyper. I want to import the file into Plink to create a .raw and .map which I can import to R for use with the adegenet package.

My plink1.9 command line is: 

./plink --vcf SNPs_34_combined_filtered.vcf --allow-extra-chr --double-id --biallelic-only --vcf-filter GATK_HQ_fail --recode A --out SNPs_34_combined_filtered 

The error I get is 

--vcf: 432k variants complete.Error: Too many distinct nonstandard chromosome/contig names.

The reference I used for SNP calling in GATK was a denovo assembled fasta with 9979 scaffolds

Thanks for any help

[Christopher Chang]

PLINK is limited to about 5000 contigs by default.  However, I can send you a high-contig build raising the limit to about 65000.

[Thomas Hartwig]

Thank you so much. I send you a message. Please let me know which way you could send me the build.

Thanks,

Thomas

[Thomas Hartwig]

Thanks a lot,

The new build worked perfectly.

Thomas

On Thursday, February 26, 2015 at 9:52:21 PM UTC-8, Thomas Hartwig wrote:

[Robert Fitak]

I am also interested in the version (build) for a larger number of scaffolds.  Are you willing to share this version?
Bob

[Christopher Chang]

I haven't been posting that build regularly since >5000 contigs is an uncommon use case that plink isn't really optimized for, but I can send you a copy if you let me know what operating system you need it for.

Alternatively, if you want to build it yourself, change MAX_POSSIBLE_CHROM to 64000 and uncomment "#define HIGH_MAX_CHROM" in plink_common.h.

[Xinhui Wang]

Dear Thomas,

do you mind to share the rebuild version of plink with more ontigs with me?

With best regards,

Alex

 

 

On Friday, February 27, 2015 at 6:52:21 AM UTC+1, Thomas Hartwig wrote:

[Christopher Chang]

I've sent the build.

For future requests of this sort, send me an email specifying the operating system you are using.

[zhao wei]

Can you send me a copy of plink for a larger number of scaffolds? My system is Cent OS. I need linux x86_64. Thank you.

在 2015年3月23日星期一 UTC+1下午7:04:03，Christopher Chang写道：

[AMK]

Hi Chris,

Would I also be able to get a copy of this plink build that can handle large numbers of contigs?
I use linux (on ubuntu 14 trusty).

Thanks!

Anna

[Christopher Chang]

Enough people have requested this that I will go ahead and raise the contig limit to ~65000 in the next stable build (which will hopefully be ready by early next week).

[Stéphanie Arnoux]

Hi Christopher Chang,

I am using Mac_OS and Unix and would like as well to solve the Error: Too many distinct nonstandard chromosome/contig names.

Can you let me know where and when it will be possible to get the next build.

Thanks a lot,

S

[Christopher Chang]

I'm hoping to have it ready within the next 48 hours, and will post another message here when it's up.

[Christopher Chang]

The contig limit has been raised to ~65000 in the 23 February development build.  If nobody reports any problems with this in the next few days, the change will make it into the stable build later this week.

On Tuesday, February 23, 2016 at 2:53:29 AM UTC-8, Stéphanie Arnoux wrote:

[Stéphanie Arnoux]

I don't know if people do that usually!!! But THANKS a lot!

Le vendredi 27 février 2015 06:52:21 UTC+1, Thomas Hartwig a écrit :

[Stéphanie Arnoux]

Hi all,

Other question related I guess to the previous one, what about the --pca option? My eigenval outpur is just made out of 0 when I force it to run by adding --allow-extra-chr.

is it possibly linked?

Thanks,

S

Le vendredi 27 février 2015 06:52:21 UTC+1, Thomas Hartwig a écrit :