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Update to GATK4 #278

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hassanfa opened this issue Feb 7, 2020 · 1 comment
Closed

Update to GATK4 #278

hassanfa opened this issue Feb 7, 2020 · 1 comment
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hassanfa commented Feb 7, 2020

Is your feature request related to a problem? Please describe.
Missing mutations with gatk3.4

Describe the solution you'd like
Mutect2 with filter variants

Describe alternatives you've considered
N/A

Additional context
Investigate usefulness of IndelRealigner and BaseCalibration with GATK4

Expected output for the feature
an annotated SNV.somatic.<case_name>.mutect.vcf.gz just like before.

Current BALSAMIC version
balsamic --version
@hassanfa hassanfa added the Feature New feature label Feb 7, 2020
@hassanfa hassanfa self-assigned this Feb 7, 2020
@hassanfa hassanfa mentioned this issue Sep 9, 2020
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updates from cancer bioinfo meeting: GATK4 is removed from BALSAMIC we don't need this anymore

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