Comments (5)
@hjt1129 Yes, it's not a perfect solution. It definitely complicates annotation and comparison. You would need to either reverse the splitting before comparing with the gff or perform the same split on the gff in order to compare.
We'd like to support CSI for vcf but we haven't had the time to do so.
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hi, we have also meet this problem. So one question is, if we split the large chromosome in reference genome, the final location information of SNP on splitted chromosome will be different with the gff annotation file of previous vision reference genome?
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I have also run into this problem trying to use VariantQC for a VCF based on a wheat genome. These very large plant genomes require csi indices. Any chance to support this from your side? Plant world is catching up with sequencing ;)
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Related Issues (20)
- Nashorn engine removed from OpenJDK 17 causes htsjdk to throw exceptions HOT 2
- Question: how to code a GTFCodec beside of the existing GFF3Codec HOT 1
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- CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed). HOT 1
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- Race conditions accessing CRAM's reference data through ReferenceSource
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- Histogram class uses unsafe methods for returning min/max
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- Escaped doublequotes in INFO descriptions result in invalid VCF file HOT 2
- Question: How to generate FAI files and TBI files HOT 5
- SamReaderFactory should use current defaults when makeDefault() is called
- Error when reading a VCF 4.3 file with spaces in INFO field values HOT 1
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