tobiasrausch / wally Goto Github PK

Hi,

Greate tool ! It would be awesome if you support http and s3 protocol .
Htslib already supports this. It may be helpfull :http://www.htslib.org/doc/htslib-s3-plugin.html

wally region -r chr3:232-4234  s3://path/bucket/test.bam -g hg19.fa

Hi, @tobiasrausch

I just wondering what's logic for order of reads in the wally region? Could we specific the order ?

Dear,

Paired-end view screenshots now shown in main github section is not showing.

Best,

Roberto

Hi @tobiasrausch,

Wally is super straightforward to use, thanks! Quick question, please: is there any way of showing all supporting reads for an specific SV? Or at least, to increase the number of displayed reads (maybe collapsing them as IGV does).

For example, this should be an inversion (turquoise color) supported by three reads but I can only see two of them... ideally I'd like to see everything.

Thank you.

Dear,

bioRxiv 2022.02.20.480758

Not going to wally manuscript.

Best,

Roberto

Hi,

Is it possible to load multiple annotation resources (gene, repeat, histone markers etc. ) in the layer for wally region to infer the functional region?

Hi,

wally speed is really impressive for a large bam. I am using it to visualize the whole genome alignment bam, so the contig could be chromosome-scale. But I found one region's display is inconsistence with IGV. I thought it was because the insert size cutoff, but I still couldn't go the same result even if I low / up down the -m.

# Wally version: v0.5.8
# using Boost: v1.74.0
# using HTSlib: v1.17

wally region -g ref.fa -b gene.bed.gz -x 2048 -r Chrx:x-x align.sorted.bam
wally region -g ref.fa -b gene.bed.gz -x 2048 -m 0 -r Chrx:x-x align.sorted.bam
wally region -g ref.fa -b gene.bed.gz -x 2048 -m 100 -r Chrx:x-x align.sorted.bam

Hi, @tobiasrausch

Is there any options in wally could turn off the coverage track? If I cannot sort the order of the reads, then each track could be too high for visualization and need to increase to a very large -y. Otherwise, wally will stop after the Image height is too small!.

So it would be possible to turn off the coverage track and set each track height separately?

Dear authors,

I downloaded the wally.sif but it doesn't seem to actually take options/ commands other than displaying the following when i execute it. Any suggestion will be much appreciated. Thanks!

Commands i tried:

$ .wally_v0.5.7.sif 
$ .wally_v0.5.7.sif region -R regions1.bed -g GRCh38.d1.vd1.fa 1T_WES.realn.bam

Output:

**********************************************************************
Program: Wally
This is free software, and you are welcome to redistribute it under
certain conditions (BSD License); for license details use '-l'.
This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'.

Wally (Version: 0.5.7)
Contact: Tobias Rausch ([email protected])
**********************************************************************

Usage: wally <command> <arguments>

    region         plot genomic region
    matches        plot read or contig alignments
    dotplot        plot pairwise alignments
    hilbert        plot genomic region as hilbert curve

Hi Tobias,

im trying to plot a simple example of mine, using this code:
/mnt/data/Tools/wally/src/wally region -R new_regions.bed -g Wheat.Svevo.CHROMOSOMES.fasta G305sv2.sorted.bam
im getting an error:

[2022-Nov-03 14:38:56] wally region -R new_regions.bed -g Wheat.Svevo.CHROMOSOMES.fasta G305sv2.sorted.bam 
[E::sam_hrecs_update_hashes] Duplicate entry "Chr1A" in sam header
Invalid region Chr1A:1400289-1400389
Chromosome not found in BAM file.

I checked the chromosome names, seems to be OK.
hope its clear,

thanks,

Yael