Himawari
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Activity overview
Latest activity by Himawari-
Himawari created a post,
GenotypeGVCF Output Only 1 Locus
Can you please provide a) GATK version used: 4.1.7.0Hello, I have this problem with genotyping my GVCFs. As you can see from the error below, only 1 locus was genotyped and the vcf produced. I have...
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Himawari commented,
Hi Bhanu GandhamI am not sure what happened. I re-run the the script again after giving up for a day and it became successful. I did not change anything from the script except for the reference gen...
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Himawari commented,
Samuel Lee Hello, it works!! Thank you~ I hope that edited .yml file is used in the next update instead of the current one. But thank you. James White It was indeed empty. After I went through th...
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Himawari commented,
Samuel LeeHello, sorry to budge in but I am having the same problem with the .yml file too Ubuntu 18.04 LTSconda 4.8.3python 3.7 conda env create -f gatkcondaenv.ymlCollecting package metadata (rep...
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Himawari commented,
Hi Bhanu Gandham Here it is (these 2 are unsuccessful..the difference between these 2 are that one the 1st set's was merged at FASTQ file stage; the 2nd set was merged at BAM file stage): @SQ SN:ch...
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Himawari commented,
Hi @Bhanu Gandham, Thank you for your reply. I actually went through the links you provided quite a lot trying to make sure that I got things right before creating an account to post here. While I ...
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Himawari created a post,
Read Group: ID for split files of multiple samples on multiple lanes
Hello,I am currently using the GATK version 4.1.4.1. I am a bit confused on how should I build my samples' read groups using the AddOrReplaceReadGroups command.My situation is that I have 5 differe...