CrossMap
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liguowang
CrossMap is a python program to lift over genome coordinates from one genome version to another.
I filed an [issue on this in bioconda](https://github.com/bioconda/bioconda-recipes/issues/25991). Briefly looking at [their recipe](https://github.com/bioconda/bioconda-recipes/blob/da52f05f3caac623e6d9cdd1a8e76afb424393f8/recipes/crossmap/meta.yaml), this issue has to do with file source used. I think it needs to be updated from...
Because Crossmap supports INFO/END values in SV VCFs since `0.4.3`, it gives the impression that it supports lifting over of structural variants as well. However it currently doesn't convert values...
`CrossMap` version 0.3.8 installed with ```python pip install CrossMap ``` using Python 3.5.2 throws the critical error ``` Traceback (most recent call last): File "CrossMap.py", line 27, in from cmmodule...
Hello. I am getting the following KeyError message: > @ 2020-08-09 09:47:32: Read the chain file: GRCh38_to_GRCh37.chain.gz @ 2020-08-09 09:47:34: Updating contig field ... @ 2020-08-09 09:47:34: Lifting over ......
Presently, CrossMap does not update the VCF header when lifting over VCF. It would be great if the old contig lines could be filtered out and replaced with the new...
Hi, in multiple occations, CrossMap does not seem to remap gene and mRNA lines from the input GFF file despite transferring exon and CDS lines for that particular gene. Does...
Dear author, First: thanks for creating and maintaining this tool as it seems the only properly working alternative for liftover. I did liftover of both a vcf and bam file...
Hi, I would like to liftover some bam files. But I got some errors when testing: ```shell # input cmd CrossMap.py bam test.chain test.bam # logs and errors Insert size...
Hi, thanks for making crossmap! I noticed a bug where it would crash when trying to lift over a VCF file that had missing alt alleles. This small patch should...
