CrossMap
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liguowang
CrossMap is a python program to lift over genome coordinates from one genome version to another.
Dear Authors, Thank you for this great tool! I have been testing CrossMap with DBSNP v151 data and found one type of conversion that doesn't look correct. For DBSNP rs202079816:...
I have a BAM that has been filtered down to only primary alignments, but after running it through CrossMap, some of the reads get labeled with the "not primary" SAM...
**Hello, Last week I was using version 0.5.3 on COLAB and was fine. I tried today the same code with the same data, but got this error:** 2021-11-23 04:48:11 [INFO]...
CrossMap v0.5.4 outputs fake data when it failed to convert the data. $ `CrossMap.py vcf mm39ToMm10.over.chain.gz test.vcf mm10.fa out.vcf` - mm39ToMm10.over.chain.gz: `https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToMm10.over.chain.gz` - `test.vcf`, `out.vcf`, `out.vcf.unmap`: I attached it. [test.vcf.gz](https://github.com/liguowang/CrossMap/files/7114004/test.vcf.gz)...
And some are not necessary at least. Have a look, please.
Hi Liguo, Is this github is latest 0.5.4 version? 4/16/2021: Release version 0.5.3/0.5.4 Add CrossMap.py viewchain to convert chain file into block-to-block, more readable format. https://crossmap.readthedocs.io/en/latest/index.html#compare-to-ucsc-liftover-tool Thanks Shicheng
Greetings! I have encountered error while installing Crossmap. Command: pip3 install CrossMap Error message: Using cached pyBigWig-0.3.17.tar.gz (64 kB) Requirement already satisfied: numpy in /home/asma/.local/lib/python3.8/site-packages (from bx-python->CrossMap) (1.19.2) Requirement already...
Do we have practice protocol for hg19 PLINK (BED/BIM/FAM) to hg38 PLINK (BED/BIM/FAM)? Thanks. Shicheng
Hi! Thanks for building the tool. I used crossmap to liftover VCF from hg38 to hg19. Some variants in the original VCF has REF as minor allele, ALT as major...
Currently CrossMap does not remove `alt_variant == ref_variant` when there are 2 alt variants. It's the VCF's fault because that is hardly a variant, but I thought that you should...
