LD heatmap no error but no colorful squares in png

[lepisorus]

Dear Tassel developer

I am using Tassel 5.2.23 command line on linux Redhat platform. 

My commands run well and it generated ld.png. But, the figure did not tell me anything. Please see the attached file for the png and standard output file. I also enclose my command line here.  

Any comments are very appreciated.

Thanks!

start3=80000000

end3=84000000

vcftools --vcf MexLow_MexHigh.recode.vcf --chr 3 --from-bp ${start3} --to-bp ${end3} --recode --out MexLow_MexHigh.chr3Inversion

run_pipeline.pl  -Xmx240g  -fork1 -importGuess MexLow_MexHigh.chr3Inversion.recode.vcf -ld -ldd png -o chr

3_inversion_ld.png

[Terry Casstevens]

I think by default -ld does a sliding window size 50, so that'd be a
narrow diagonal. And your -ldd default image size is small.

See this for options
https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/Tassel5PipelineCLI.pdf

And specify -ldplotsize

Best,

Terry

> --
> You received this message because you are subscribed to the Google Groups
> "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to tassel+un...@googlegroups.com.
> To post to this group, send email to tas...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/tassel/0e018502-beca-4eed-bc96-d96c4df4e77f%40googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

[lepisorus]

Thanks, Terry! I will try tuning the parameters. 

Best

[lepisorus]

Hi, Terry

I experimented to increase my -ldWinSize to 1000 and 5000, the -ldplotsize to 4000, but it still gave grey pictures. Is this owing to too many SNPs within this region (43884) and thus too many comparisons? I am not sure if I am going in the right direction. Thank you very much for your insights!

Best

Li

On Tuesday, February 28, 2017 at 10:34:59 AM UTC-6, Terry wrote:

[Terry Casstevens]

Please update to the latest release of TASSEL. Try this command.

./run_pipeline.pl -Xmx240g -importGuess
MexLow_MexHigh.chr3Inversion.recode.vcf -ld -ldType All -ldd png
-ldplotsize 5000 -o chr3_inversion_ld.png

> https://groups.google.com/d/msgid/tassel/c0323e8c-5fd3-4654-922b-b4b7546a81bc%40googlegroups.com.