Comments (5)
lbergelson
commented on September 12, 2024
1
@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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hjt1129
commented on September 12, 2024
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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jd3234
commented on September 12, 2024
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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