
New_gatk_user
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Activity overview
Latest activity by New_gatk_user-
New_gatk_user commented,
Many thanks again for pointing out some helpful discussion links. I'll continue to look for ways to resolve. Best.
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New_gatk_user commented,
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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New_gatk_user commented,
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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New_gatk_user created a post,
Haplotype caller error; java.lang.IllegalStateException: Graph must have ref source and sink vertices
AnsweredHello! I am using GATK 4.1.7.0 to call SNPs per-sample but have run into an issue I don't know how to resolve. I have several haploid samples and the Haplotype caller's run to produce GVCFs doesn't...
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New_gatk_user commented,
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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New_gatk_user commented,
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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New_gatk_user commented,
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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New_gatk_user created a post,
A USER ERROR has occurred: Badly formed genome unclippedLoc: Parameters to GenomeLocParser are incorrect:The stop position 0 is less than start 1 in contig contig004333
AnsweredHi There, I am trying to run gatk-4.1.7.0's Haplotype caller and I keep getting this error; "A USER ERROR has occurred: Badly formed genome unclippedLoc: Parameters to GenomeLocParser are incor...
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New_gatk_user commented,
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...
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New_gatk_user created a post,
Calculating the empirical allele frequency
Hello! First off is to just let you know that the GATK forums site is down. For the whole of this last week of July, 2020, I have been trying to access answers from past questions posted in the for...