variant phred scale of plant genome

Question

[rastogi.suraj93]

Hello every one,

I appreciate if any one tell me what is good parameter of SNP calling for Plant genome analysis??

Thanks to all Regards Suraj Rastogi

[Fabio Marroni]

Dear Rastogi, it is very difficult to answer to your question. You have several parameters to set for performing SNP calling (and actually you also have to decide which software to use, and which sample, and so on), and we do not know anything about the data set you have. I think you should specify better the quastion, otherwise you will not get help!

I suggest you read the guide on how to ask good questions on biostars, and if you want I found here on biostars a tutorial on SNP calling that maybe can help you

Good luck!

[rastogi.suraj93]

Dear marroni, thanks for reply.. now I mention every thing of my work u can check and suggest me depend on my query..

[Brian Bushnell]

I recommend the parameter "--help", which works on a variety of different tools.

[harold.smith.tarheel]

Awesome answer - short and sweet!

[User 59]

Plants come in a variety of ploidys. Calling variants on a diploid plant is not going to be the same as calling variants on an octoploid plant, consequently it's going to be hard to give you a generalised answer.

[laibazoologist]

Dear all i want to know about evolutionary time period (mya) please help me to finding the milion years ago in phylogenetic tree?

[ATpoint]

Please do not ask questions in old threads. Open a new one following the suggestions in Brief Reminder On How To Ask A Good Question

Answer 1

[rastogi.suraj93]

dear all, i am using samtool, bcf tool and vcf tools for variant calling of hexaploidy plant data which is sequenced by illumina hiseq 1000 and read length is 83 bp.this is paired end data. and also using snpEff for variant filter from vcf file by different parameter like QUAL>30 and DP > 10. 1- samtools for calling all variant 2- bcftools for only view genotype variants 3- snpEff for filter genotypic variant based on variant depth DP>10 and variant base quality QUAL >30 and remove other below on this parameter. 4- vcf tools for count variation like SNP and INdel.

So i want ask to all what is the standard parameter for filter true SNP and indel? whatever i used for true SNP is ok or need to change something? thank you..

[WouterDeCoster]

Setting such a cutoff is a trade-off between sensitivity and specificity, so it depends on your application, e.g. would you like to find all potential variants or preferably only those with high confidence...

[rastogi.suraj93]

ok... thanks to WouterDeCoster.