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Can we use GraphAlignmentViewer for Expansion hunter denovo result viewing using locus specific bamlets?

Hi @virajbdeshpande
ExpansionHunter produced genotypes (for the same sample) at 10x, 15x and 30x, but in GraphAlignmentViewer genotype is given only for 10x and not for 15x and 30x. Input used was the realigned bam file from Expansion Hunter in each case and variant catalog. (Was run as a single sample at each coverage). Why is it so & how to view genotypes at 15x and 30x too?

Hello, I'm running GAV on the input/output of the example bundled with the latest ExpansionHunter. It runs in 1 second without errors but no output, no output whatsoever, anywhere. Any ideas?

python3 ~/Programs/GraphAlignmentViewer-master/GraphAlignmentViewer.py --variant_catalog $(realpath ../variants.json) --read_align $(realpath ../../output/rr.sorted.bam) --gt_file $(realpath ../../output/repeats.json) --output_dir .

pip3 list | grep -i 'pyyaml\|pysam\|matplotlib\|numpy'
matplotlib 3.3.4
numpy 1.19.5
pysam 0.18.0
PyYAML 6.0

GAV has no --version option, and there is no version mentioned in any of its scripts, but I am using the latest version as of last week.

Grateful for help!

Hi

Thank you for creating this great platform to investigate and visualize STRs. I need help with further interpreting and understanding EH results on GraphAlignmentViewer. Maybe I’ve missed this and it has been posted elsewhere, but wanted to know what do the lower-case nucleotides indicate in GraphAlignmentViewer. For instance, in the example that is provided on the GraphAlignmentViewer github page, there are some bases in alignments that are lower-case:

(https://github.com/Illumina/GraphAlignmentViewer)

Would this indicate soft-clipped bases (which are different from SNPs)?

For example, #2 was difficult to debug since it did not tell me how many and which sites it was outputting (it output none).

Hi
I am using this tool to view my EXPHunter results.
I observed that some png files for eg ATN1:CAG or DMPK were cropped while others HTT were fine. It seems that since these alleles were shorter in sequence, its consequent image was affected while for longer alleles it wasn't.
How can I resolve this?

Also, is there any interactive viewing tool with similar functionality as GAV?

Hi,

I have been using your tool to visualize BAM files produced by Expansion Hunter.
For most BAM files produced by Expansion Hunter visualization works fine. But in some cases, I noticed that GraphAlignmentViewer is not showing full allele length predicted by Expansion Hunter. Can you explain to me what I am doing wrong?
I am running commands --variant_catalog, --read_align and --vcf with appropriate files.
I also tested two more parameters --region_extension_clip_length and --show_insertions, but I still don't get the full length.
Thank you