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DP/AD in SNP greater than coverage in bamout?
Hello, I have a question: how can the DP or AD at a particular site be (much) greater than the coverage at that position in the reassembled bamout file? I see many examples of this, for example the...
Hello, I'm wondering if this is a bug. Please see the variant called by GATK HaplotypeCaller below. There are 6549 reads supporting the alt allele, and only 1 read supporting the reference allele. ...
Haplotypecaller pooled sample unknown number of samples
Hello, Wondering if there is a GATK haplotypecaller equivalent of freebayes --pooled-continuous option for pooled samples where the number of samples is unknown? Thank you very much.
How is AC calculated?
I am having trouble understanding how AC is calculated. Please see the following 2 lines in a VCF: X 2234 . A G 110933.03 PASS AC=2;AF=1.00;AN=2;DP=2914;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00...
multiple vcf files in FastaAlternateReferenceMaker
Hello, The documentation here https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker states that for input: The reference, requested intervals, and any number o...
Pre-trained architecture for CNNScoreVariants and non-human dataAnswered
Thank you for this great tool. I was wondering if the pre-trained architecture would be suitable for non-human data, or would it be better to stick to hard filtering?
Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
I would like to resurrect the issue described here which was never answered definitely: https://gatkforums.broadinstitute.org/gatk/discussion/13127/do-gatk4-tools-ignore-vcf-sites-marked-as-filtere...