BQSR CNN sketch #21
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BQSR CNN sketch #21
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takutosato
reviewed
Sep 19, 2018
api_tutorials/bqsr_cnn.py
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| bed_dict = bqsr_bed_file_to_dict(args.bed_file) | ||
| record_dict = SeqIO.to_dict(SeqIO.parse(args.reference_fasta, "fasta")) | ||
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| margin = args.window_size/2 |
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It looks like pysam's fetch() captures all reads that intersect the [start,end] interval. So the current code is capturing many reads that have NIST variants. We should get somewhat better empirical quality if we get rid of the /2.
This reverts commit e1bde7c.
…sidual connections
…till not working properly
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@yfarjoun @fleharty @takutosato BQSRing with CNNs.