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Hi Sheila, Thanks very much for your answer. But can you tell me which version should I use as I need this summary table. Or how can I Calculate the Actual calls made and Confidently called bases? I see that the Tools you mentioned above, I c…
Hi Sheila, Thanks very much. Cheers, Namrata
Hi Sheila, The length of the contig in the reference genome is 1758. And when by doing samtools view -h myfile.bam | grep scaffold69676_size1796 i got @SQ SN:scaffold69676_size1796 LN:3149. These lengths are consistant with the Error message…
Hi Sheila, Thanks for your feedback. I created a new Index file and tried again but still it is giving me the same error. Do you have any other suggestions? Many Thanks, Namrata
Thanks for your feedback. I will try with the latest version. As per my knowledge, Callable bases that exceed the emit confidence threshold, either for being non-reference or reference and they should be always greater or equal to Actual calls mad…
Thanks for your reply. I will ask for a newer version. I am just wondering if the number of Actual calls made can be greater than the number of Confidently called bases ? Or this Result is wrong?
Hi Geraldine, I am using GenomeAnalysisTK-1.2-4-gd9ea764. This version in installed in the servers of Swiss Institute of Bioinformatics.