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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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adapting to GATK4 #7

Closed lucacozzuto closed 5 years ago

lucacozzuto commented 5 years ago

A number of modifications to adapt to the new style of GATK 4. I also moved the filtering of unique alignments after the mapping and added an indexing of the VCF required for ASEReadCounter.

lucacozzuto commented 5 years ago

You need to sleep more :) I used the docker with GATK4 you already have!

pditommaso commented 5 years ago

Merged manually on gatk4 branch. Thanks a lot for the contribution!