Han Cao

Hi Shuqi (@Meltpinkg), Thanks for your explanation. Now I understand why and how this happen, but I have some additional questions on it: 1. Actually I want to use INFO...

Hi Shuqi (@Meltpinkg), Thank you very much for your nice explanation and benchmark, which totally solve my problem! I will use the force calling results now. Best, Han

Hi Shuqi, That's great! Thank you so much! Best, Han

Hi, I did more research on this case, and I realized the interchromosomal misjoin could occurs within the black window. I randomly selected one position within the black window and...

@TDMillar-Biology Yes, I followed the instructions from HPRC paper, they manually split one assembly in their study, you can find more details in their paper, [hprc-v1.1 tutorial](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/mc-pangenomes/hprc-v1.1-mc.md#prepare-the-input-assembly-list), and [this issue](https://github.com/ComparativeGenomicsToolkit/cactus/issues/1389)....

I also ran into this error and found it is caused by Windows line endings. You can check the manifest file and replace all '\r\n' with '\n'

Thank you so much for the explanation! According to this [answer](https://www.biostars.org/p/9597049/#9597285), any >10 kbp parts of GRCh38 that don't align to CHM13 are missing from the graph. So, I think...

Many thanks for your suggestions. I will also try the GRCh38-based graph.

I find other issues with the output INFO of vcfwave, you can replicate this with HPRCv1.1 VCFs: - hprc-v1.1-mc-chm13.raw.vcf.gz: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-chm13/hprc-v1.1-mc-chm13.raw.vcf.gz - hprc-v1.1-mc-chm13.vcfbub.a100k.wave.vcf.gz: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-chm13/hprc-v1.1-mc-chm13.vcfbub.a100k.wave.vcf.gz ``` bcftools view -H -r chr22:11021446-11021447 -s...

Hi @ekg, I generate a small test VCF using of the above 3 examples: ``` ##fileformat=VCFv4.2 ##FILTER= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= #CHROM POS...