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Its human, not sarscov2
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apeltzer committed Oct 28, 2021
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* 'test.paired_end.name.sorted.bam': Paired-end bam file sorted by name
* 'test.single_end.bam': alignment (unsorted) of the 'test_1.fastq.gz' reads against test_genomic.fasta using minimap2
* 'test.unaligned.bam': unmapped BAM file created from 'test_1.fastq.gz' using GATK4 SamToFastq
* 'example_hla_pe.bam': Downsampled BAM file for HLATyping workflow / OptiType module. Using existing data did not work as it misses preparation steps.
* bedgraph
* 'test.bedgraph'
* bigwig
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* test2.paired_end.sorted: Mapped, and sorted reads based on `test2{,.umi}_{1,2}` (tumor)
* test2.paired_end.markduplicates.sorted: Mapped, sorted, and duplicate marked reads based on `test2{,.umi}_{1,2}` (tumor)
* test2.paired_end.recalibrated.sorted: Mapped, sorted, duplicate marked, and recalibrated reads based on `test2{,.umi}_{1,2}` (tumor)
* 'example_hla_pe.bam': Downsampled BAM file for HLATyping workflow / OptiType module. Using existing data did not work as it misses preparation steps.
* umi:
* test.paired_end.umi_*: Files base on `test.umi_{1,2}` (normal)
* test2.paired_end.umi_*: Files base on `test2.umi_{1,2}` (tumor)
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