New_gatk_user
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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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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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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...
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haploid variant reads support
Hi GATK team, I have used V. 3.8-0 of GATK's HaplotypeCaller to call haploid variants, and I have also filtered my multisample vcf file appropriately by using SelectVariants to select SNPs and Var...