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Thanks for the clarification. Indeed for haploid species, it should have only ref or alt theoretically. I got confused as for virus or even for bacteria, there is sometimes more then one population in a sample, resulting ref/alt to appear at the …
Hi, I had a question about ReadPosRankSum in haploid. I went through the definition given at GATK doc page ReadPosRankSumTest, also the explanation of the statistics behind the score at Rank Sum Test. However, I could not find any information …
Hope this page can be updated soon. Most importantly, how to setup multi-threading settings so that GATK 4 will not simply take all cores... Thx.
Are there any plan to change this? Now both bwa and bowtie2 can support mapping of both paired and single reads at the same time. And for some samples we are handling, it will be beneficiary if single reads can be handled together.
It is still not fixed in 3.7. Or I might misunderstand the function of '--removeUnusedAlternates'. When I subset on this sample, in which the INDEL is called (1st record), using following parameter (from gatk log): 'Program Args: -T SelectVar…
Hi, GATK team, Is this bug actually fixed? I tried the latest nightly build, but the issue seems still there... For my case, I need to extract variants of individual sample from a multiple sample VCF file. I used following command to do so. "…
I see. For our case, I will continue with only the paired reads in Trimmomatic result then. We will see in future whether we can skip Timmomatic step. Thanks for your time and help.
hi, Sheila, Upon seeing your reply, I tried it again on another computer, indeed they are working. It seems the issue is with the machine and/or the browser that I use. Am I sorry that I did not think of this, as I had not encountered any issue w…
Hello, This workshop is really very interesting and this is the latest one as well. I really would like to check the videos for the presentation, as not all information is in the slides. However, the videos available at http://www.broadinstitute.…