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Hello,
We are currently trying to run Anchorwave on the huge Axolotl genome (32 Gbp) and we are getting the following error:
Command:
```
anchorwave proali -t 19 -i GCF_000001405.39_GRCh38.p13…
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When converting the VCF spruce data to Zarr I noticed that even the longer chromosomes (>1.2Gbp) are encoded as 32-bit integers. In the text I wrote that the maximum value of VCF POS is ~537Mbp (God k…
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## Bug Report
### FilterIntervals
gatk FilterIntervals \
-L ${OUTPUT}/bins.interval_list \
--annotated-intervals ${OUTPUT}/bins_annotated.interval_list \
-imr OVERLAPPING_ONLY \
$INPUT…
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I am facing an issue with the GC correction. I created the gc-file using the [instructions to create a gc-file](https://github.com/abyzovlab/CNVpytor/blob/master/examples/AddReferenceGenome.md) and pr…
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Could you please drop the requirement that chromosome start with "chr" from bcftools csq. This creates many headaches when working with other species where this is not the case.
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[Dear]() Blogger,
I hope this message finds you well. I’m writing to ask for your guidance regarding an issue…
hj-99 updated
2 weeks ago
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bigwigaverageoverbed and the python equivalent give `The passed chromosome (X) was incorrect.` when a chromosome name was not found. UCSC Kent bigWigAverageOverBed does not do that.
It would be nic…
ghuls updated
3 weeks ago
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I am using Mustache to call loops on MICRO-C data mapped on human genome T2T version (CHM13/hs1)
I run each chromosome individually with this code:
E.g. For chromosome 1
mustache -f -ch chr1 -r …
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Thank you very much for creating amazing resources!
Quick question: do you plan to release phased chromosome X any time soon?
Thanks again!
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Hi,
I found that gffread (v0.12.7.) can not deal with large chromosomes, we may find minus coordinates when using gffread to deal with such large chromosomes, for example, for a genome here https:/…