Pontus Höjer

I second this, it would be a very useful addition. Also I think that being able to reads from a list of chromosomes/contigs would be useful. Specifying chromosomes by comma...

The same error appeared again in a new BibTex entry which also has a similar page field `pages = {1--4},`.

> Hi - a small typ file, or a small bib file? Both, I had the same setup. A main typ file that cites and imports a bib file. >...

Which version of `samplot` are you using? There have been quite a few additions since the latest [release](https://github.com/ryanlayer/samplot/releases/tag/v1.3.0). I would recommend installing the development version for now, using for example...

You need to provide a sample ID using the `--sample_ids` argument. This sample id should be the same as the sample name in your VCF.

> ``` >File "/vf/users/okendojo/conda/envs/samplot/lib/python3.10/site-packages/samplot/samplot_vcf.py", line 949, in >generate_commands > svtype = variant.info.get("SVTYPE", "SV") > File "pysam/libcbcf.pyx", line 2711, in pysam.libcbcf.VariantRecordInfo.get >ValueError: Invalid header >``` Seems like the VCF might not...

Thanks for providing the VCF! I see the issue now. The VCF you provide does not contain any structural variants, only short (

If by "standard GATK" you mean "HaplotypeCaller" then no. For structural variants other callers are required, examples for short reads are [smoove](https://github.com/brentp/smoove) and [manta](https://github.com/Illumina/manta). If you are allready using Dragen...

This issue should be fixed now that https://github.com/ryanlayer/samplot/pull/158 is merged.

This should be fixed now that https://github.com/ryanlayer/samplot/pull/147 is merged.