prateekg04

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prateekg04
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Prateek Gupta

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  • Hi Sheila, Thanks for you answer. But our samples are pooled samples and we can't reduce the ploidy level. initially, I tried to run it with --max-genotype-count 4 to check whether the warning comes or not, but it is giving the below mentioned erro…
  • Hi Sheila, So can you suggest me which version of GATK is good for using UnifiedGenotyper for highly pooled samples. As I am unable to detect the mutation in positive control when used GATK 3.6 but I am still able to detect in GATK 3.5 and 3.4. Re…
  • Hi Sheila, Please find the command line below used for the UnifiedGenotyper and I have put few lines from the vcf files, my positive control is GGH1-2 position 86 change G->A. As you can see there are lot of differences in the snps list identifi…
  • But I am able to run Unified Genotyper with high ploidy levels, do you think that Unified Genotyper is better in this case. Or can you please suggest any other tool or pipeline which can efficiently call rare variants in highly pooled data set. Tha…
  • I have a pooled data set, that's why I have given a ploidy of 96. I have also run this with Xmx64g but same error. Is there any other way to do this. Thanks.
  • Hi Geraldline, Thanks for the reply and sorry for incomplete information. I am using the UnifiedGenotyper, plz find the command below which i have used. As we have 64-fold pooled data set for a diploid organism, so we are using ploidy 128 for the a…