Rolf Schröder
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Activity overview
Latest activity by Rolf Schröder-
Rolf Schröder commented,
Hi James, I tested 4.5.0.0 once again as you suggested. When running with `--alleles` using the VCF from the child, the variant is revealed: 21 34923904 . C T 1457.64 . AC=1;AF=0.500;AN...
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Rolf Schröder commented,
Hey James, thank you very much for that answer. In the meantime, I had also looked for repetitive sequences and realized that this might be the culprint. Here are my results for now. I will test yo...
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Rolf Schröder created a post,
Variant not called by HaplotypeCaller (not called in father, but present in child)
Hi, I have a bam file where an expected variant (21:34923904C>T) is not called by HaplotypeCaller.I have followed the advice from https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When...
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Rolf Schröder commented,
Hey Louis, thanks a lot. This does help a lot for my understanding!
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Rolf Schröder created a post,
Haplotype calls deletion followed by insertion instead of indel
Hi, I am using the HaplotypeCaller (GATK 4.4.0.0). When I look at the input BAM file in IGV, I expect the variant NC_000015.9:g.48760182_48760185delinsGGGT. However, HaplotypeCaller reports NC_0000...