New_gatk_user
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Many thanks again for pointing out some helpful discussion links. I'll continue to look for ways to resolve. Best.
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HI Genevieve, Thank you for the links, much appreciated. However, the very last comment by Geraldine on this discussion (https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussion...
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The Haplotype caller runs successfully through many contigs so I'm not sure if I can paste the entire log here. However, I paste the last few lines just before the point where it looks like the alg...
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Hi Genevieve, Not yet, and I still don't have a clue on how to proceed/resolve. I thought maybe the issue was somehow related to my initial problem and this is why I've followed it up here. I wi...
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Hi again Genevieve, Thanks for your pointers. I looked through my entire assembly fasta file and removed the empty headers with no bases, and using this fixed assembly fasta file, I ran alignment...
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Hi Genevieve, I looked in my fasta file and I found that this specific contig and several others, didn't have any bases so it was just their headers e.g. >contig004332 AAGGGCCT ... >contig004333 >c...
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Thank you so much, Genevieve, for letting me know whats going on with the old site and for pointing me to the archived forum site. I have been pulling my hairs about this for the whole of this week...