Can Kockan
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Activity overview
Latest activity by Can Kockan-
Can Kockan commented,
Looking at your original reference index Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.fai , it seems that the contigs are using the 1, 2, ..., X, Y, MT convention unless I'm missing something. Us...
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Can Kockan commented,
Just a tiny addition to Gökalp Çelik's suggestions regarding potential whitespace issues; the last two replies on this thread might be worth checking out: https://gatk.broadinstitute.org/hc/en-us/c...
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Can Kockan commented,
Might still be a good idea, just to make sure that whitespaces, etc. don't get mangled during the download process. Your system information and the command-line you are using these files with would...
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Can Kockan commented,
Hi Nikola Antić , essentially you'll want to:- Fork the repo- Clone the fork to your system- Create a new branch for your feature- Make your changes- Push your changes back to your fork- Create a P...
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Can Kockan commented,
It might be a whitespace related issue, I recall seeing something similar here: https://gatk.broadinstitute.org/hc/en-us/community/posts/21369679658267-Tribble-can-t-find-CHROM-header-but-line-is-p...
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Can Kockan commented,
gabriele tosadori That could still be an early termination, I'd expect an exit status as well. I'd check the output VCF to make sure but I highly suspect that this is similar to the following issue...
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Can Kockan commented,
Hi UTao Cao , looking at your header it might be a sorting issue as James had previously suspected. I see that the sorting order is unknown and it is possible that your file is not coordinate-sorte...
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Can Kockan commented,
Hi Mario Fasold , I completely agree with you regarding the broken links. I've relayed this post and now there's an issue on the GATK repo: https://github.com/broadinstitute/gatk/issues/8682It prob...
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Can Kockan commented,
Hi Luo Hao , if your intention was to remove germline variants as David previously mentioned, the gnomAD germline resource should work fine. It should even be a more thorough resource than dbSNP in...
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Can Kockan commented,
Hi Charles Deng , it looks like ExtractFingerprint does not support VCF inputs at the moment. If your goal is to run either CheckFingerprint (https://gatk.broadinstitute.org/hc/en-us/articles/21904...