Unable to convert hg19 to hg38 in bed file. And not taking optional arguments

[jporton]

I've tried several options and it always fails. Originally it wouldn't accept one of the strand directions "." so I removed that column, and even shortened my bed file to a bed3 and I continue to have issues.

It also will not take additional arguments of --chromid. I've tried several formats, when I try to give it these optional arguments I just get the help page.

Here is the output from one of my attempts to convert

(/HPCPool/shared/conda_envs/microhap) CrossMap.py bed hg19ToHg38.over.chain.gz QIAseq_Microhaplotype_target_regions.bed3 
@ 2022-11-23 09:08:57: Read chain_file:  hg19ToHg38.over.chain.gz
1 3743315 3743396       Fail
1 18722784 18722850     Fail
1 161955750 161955808   Fail
1 230820574 230820634   Fail

[liguowang]

Hello, Can't figure out why it failed. Here is what I get.

$CrossMap.py --version CrossMap 0.6.4

$cat test.bed 1 3743315 3743396 1 18722784 18722850 1 161955750 161955808 1 230820574 230820634

$CrossMap.py bed GRCh37_to_GRCh38.chain.gz test.bed 1 3743315 3743396 -> 1 3826751 3826832 1 18722784 18722850 -> 1 18396290 18396356 1 161955750 161955808 -> 1 161985960 161986018 1 230820574 230820634 -> 1 230684828 230684888