RUIXUE LIU

I have the same question as dd2019d. I only have the reference genome of my research organism in `.fa` file and long-reads sequences of several samples in `.bam` file. I...

> To make a pangenome from long reads you can either: > > 1. Create a VCF using a _variant caller_, then use `vg construct` or > 2. Use an...

According to [an answer](https://www.biostars.org/p/9527307/#9527323:~:text=they%20seem%20to%20check%20for%20a%20TBI%20or%20CSI%20file%20(https%3A//github.com/vgteam/vg/blob/2c36d2cd08bef668eca2a8a64ba51abc037c905b/src/index_registry.cpp%23L561)%20before%20the%20error%20message%20though%2C%20so%20I%20don%27t%20know%20what%27s%20happening.) on biostars forum, vg seems trying to check if csi exist before the error msg.

Yes. no idea if this issue appears results from vg not supporting csi. If so, that is really bad news for me.

Is there a plan to let vg supports csi? Or Any suggestions for my case?

> The index is built with tabix, and its default is a TBI index, which cannot work with some chromosome lengths. Since you are already using a CSI index for...

> Hmm, searching more about this brought me to [pysam-developers/pysam#995](https://github.com/pysam-developers/pysam/issues/995) That bug is fixed in pysam 0.17.0. Can you see which one you have? pysam version in my environment is...

> Yes, and then I expect it to actually build a CSI index, and not ignore that argument as in v0.16 hooray! The CSI index generate successfully! There is just...

@fritzsedlazeck Hi, Fritz. Thank you so much for the response! Can I absorb your explanation in the way that, the bcftools merge would give me more variants including some rare...

还在抢救，这贴关了吧