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Genotype complex variants including complex indels #3

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andurill opened this issue Feb 10, 2020 · 0 comments
Open

Genotype complex variants including complex indels #3

andurill opened this issue Feb 10, 2020 · 0 comments

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@andurill
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Complex indels such as the ones in the attached images should be genotyped based on the entire sequence of provided alt contigs. Currently, I believe its genotyped as positive if the first base of the alt contig is present in the reads.

Additionally, GBCM should not trim any putative anchor bases on the REF and ALT sequences provided in the maf format.

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@andurill