CrossMap
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liguowang
CrossMap is a python program to lift over genome coordinates from one genome version to another.
Hi CrossMap Devs, What a nifty tool! I'm writing to report that `CrossMap gff` is writing feature start and end coordinates in floating point values instead of integers in the...
Hello, Thanks for this useful utility. I have data in MAF format (NCBI build 37). I am trying to lift it over to hg38 using the following Crossmap (v0.6.6) command:...
Hi, After installing CrossMap with pip, running `python -c 'help("modules")'` yields: ``` Please wait a moment while I gather a list of all available modules... Segmentation fault (core dumped) ```...
https://github.com/liguowang/CrossMap/blob/bee595c8d1598c79e1f9933a8c02473e2bfc0630/src/cmmodule/mapvcf.py#L197-L222
Hi, I have read all your responses to question relating to "VCF" liftovers. I understand the literal meaning of "CrossMap does NOT check if the reference allele is different from...
hi wang i crossmap gvcf 2 hg38 ``` CrossMap.py gvcf /disk/reference/liftover_ref/hg19ToHg38.over.chain M248.g.vcf.gz /storage/data/reference/update_gatk_v0/Homo_sapiens_assembly38.fasta crossmap_HG38/M248.g.vcf.gz_HG38.g.vcf.gz --compress --chromid l ``` version = 0.6.6 ``` 2023-11-07 05:04:03 [INFO] Updating contig field ... 2023-11-07...
Hi, I've been using your CrossMap for a while to convert the gene coordinates of chimpanzee and orangutan to human's one, thanks to you! It's been working so far very...
Dear Crossmap Maintainer, I am reaching out to report an issue I've encountered while using Crossmap. I was trying to liftover my VCF file from T2T to hg38, but found...
Hi Dr.Wang! CrossMap is an excellent tool that has helped me a lot! However, because it requires some dependencies at runtime and some bottlenecks in the python language, its execution...
Hello. I am just wondering what version of GPL CrossMap is licensed under. Thank you for a wonderful tool. Anders.
