Open Duda5 opened 1 year ago
Insertions are not currently supported by Samplot, but we are in the planning stages of implementing them. As for the deletions, can you try plotting some individual regions from the VCF with samplot plot
?
Also, based on the error, check the sample name in the VCF and see if it matches the sample name in the BAM
Thanks for prompt reply, @mchowdh200!
The sample name in the the VCF file was correct, but I noticed that there was no @RG
tag in my bam file.
I used samtools addreplacerg
to add it back and it works now!
However, I have another issue.
I prepared the .gff3
file and indexed it as recommended (but I used Homo_sapiens.GRCh38.107.gff3.gz
version as I aligned my reads to hg38).
So, I have the annotation column in the index.html
file:
But none of the images actually contain the gene track.
For examples this deletion that has an overlap column value
gene
:
I supplied sorted gff3 file via --gff3
flag, so I am not sure why the track is not displayed below the coverage plot.
From the usage string, I saw this description for the --gff3
option
used when building HTML table and table filters
(default: None)
This leads me to believe that it's used for some sort of table filtering and not for plotting the track. In samplot plot
we have the -T
option for plotting the gff track underneath the samples, but it doesn't seem to be part of samplot vcf
yet.
This leads me to believe that it's used for some sort of table filtering and not for plotting the track. In
samplot plot
we have the-T
option for plotting the gff track underneath the samples, but it doesn't seem to be part ofsamplot vcf
yet.
It is actually possible to add additional samplot plot
arguments to samplot vcf
that will be passed on to each samplot plot
call. For the command above it would be something like:
samplot vcf --vcf HG033_sniffles_SVs.vcf -d . --sample_ids HG033_sniffles -b HG033_hg38_mnp2.bam --plot_all --gff3 Homo_sapiens.GRCh38.107.gff3.gz -T Homo_sapiens.GRCh38.107.gff3.gz
I generated a
vcf
file withsniffles
(on PacBio HiFi reads aligned to hg38) and I am trying to visualize SVs usingsamplot vcf
(conda
installation).vcf
file stats:samplot
command I used:samplot vcf --vcf HG033_sniffles_SVs.vcf -d . --sample_ids HG033_sniffles -b HG033_hg38_mnp2.bam --plot_all
But the output is only an emptyindex.html
file.When I include a
--debug
flag, there are 2 recurring types of errors: 1) For INS -INS type not supported
I have seen this error in other raised issues and if understand it correctly,samplot
does not visualize SNPs 2) For DEL (of any size) -no plottable samples with matched alignment files
What can be causing that?Also, I do not understand why longer insertions and other types of SVs are not visualized.