samplot

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cant tell how much supporting evidence.

1

the way the discordant and split reads are drawn, it's not easy/possible to tell how much evidence there is for a particular event since all linse are drawn on top...

brentp

Would be nice if `samplot_vcf.py` could produce a result like the following, which shows long- and short-read alignments for a single sample at various regions in the genome. Currently, `samplot_vcf.py`...

petermchale

e.g. from gnomad or CCDG

brentp

see this example where the splitters are pretty well hidden because they are inside $n std deviations. 

brentp

This problem arises for large-ish variants having both SR and PE support. The alignments become layered on top of one another making it somewhat difficult to tell if both types...

arq5x

Split view coordinates annotated incorrectly

1

Hi, I have noticed an issue where the coordinates for split view plots seem to be incorrect. For instance, in one of your examples here https://layerlab.org/2019/06/04/Samplot-improvement.html: The deletion was generated...

Y-Pei

plot with transcripts error

2

I've downloaded, sorted and indexed the gff3 file from ensembl, but when I use it with samplot plot -T I get the following error: ``` $ samplot plot -c chr14...

abrusell

Issues with using the samplot vcf module

3

Dear Samplot Development Team, I would like to express my gratitude for developing such a valuable tool like Samplot. Your efforts have significantly contributed to the research community, and I...

karen916

how to obtain read names / co-ordinates to inspect on IGV

3

Hello, this is great, and apologies if i am missing something obvious. I have CNV calls based on single cell low coverage WGS, with boundaries very imprecise, and trying to...

proukakis

svtype = variant.info.get("SVTYPE", "SV")

6

I am getting the following error and I am not sure how to go around this. I used the following command to annotate the my vcf. `duphold -v macope2_sorted.vcf -b...

okendojo