asylvz / svarp Goto Github PK

Hi,
I'm looking at your paper, but there are some questions I don't understand.

In the step 5, Svtig2 is aligned to the s6 and s7 nodes, but why is SVtig2.1 >s6, SVtig 2.2 >s8 shown in Alignments？And why not use 'SVtig 2 >s6>s7' as the SVtig1 shown?

Can you help me explain it, thank you.

Hi @asylvz , svtigs is a cool representation, but I still have some questions about it:

how to get the breakpoints or call variants? My process is aligning svtigs.fa to ref.fa, so that I could get the variants of ref.

But how about the non-reference path? After got the variants of some_path, how to augment the original graph by using this non-reference variants ?

Sincerely Looking forward to your answer :D

Best regards,
Wenjie

Hi,
So excited to see this pangenome-based SV caller! Would you please give me some detailed information to use svarp?

1. An alignment file in .gaf format is needed, I wonder which aligner is suitable for svarp, GraphAligner or minigraph? Is there any tools and parameters recommended to align the sequence to a GFA graph ?
2. Does the input parameter --fasta (-f) mean the query sequence? The .gaf file is already provided, why do we need the fasta file as well? Is it to provide insertion sequence information?

Thanks

-Zoey

Hi @asylvz ! thank you for creating such a valuable tool!

However, I encountered some problems in the process of using it. The following are my specific steps:

1. generate graph by Minigraph-Cactus to integrate hg38 & chm13 & new-assembly, and we chose the intermediate graph, which is the output of minigraph.
2. PacBio HiFi long-reads alignments by minigraph -cx lr --vc ref.gfa reads.fa.gz > align.gaf
3. run svarp: svarp -a align.gaf -g ref.gfa -f COLO829.T1.fa.gz -o svarp_out

But svarp didn't return success, and here is log file:

Using wtdbg2 for assembly...
No phase information provided (--phase). SVs will not be phased...

...hallo, merhaba, ola, salaam, hello!!! SVarp is running...

Parameters:
	Minimum read support: 5
	Minimum distance threshold: 100

	Minimum map ratio: 0.9
	Precise clipping (Graphaligner): 0.97
	Alignment score (Graphaligner): 5000


Input files:
	COLO829T1_grch38.t2t.COLO829N1.sv.gaf
	grch38.t2t.COLO829N1.sv.gfa
	COLO829.T1.fa.gz

Log folder:
	svarp_out/

Reading the GFA file
Reading the GAF file
--->execution time: 224.996sec.
--->5676320 primary mappings and 32517 insertion, 38672 deletion loci in the cigar
--->there are 487014 SV signal (85039 inter alignment and 401975 intra alignment)
--->there are 0 unmapped alignments

Merging nearby SV signals
--->51498 read clusters (putative svtigs) after merging and
--->5370 read clusters after filtering based on minimum read support


Assembly...
--->assembling reads using wtdbg2
--->1235 filtered (674 high, 561 low coverage read clusters and 0 low read support)
--->0 clusters cannot be assembled
--->there are 0 svtigs before final filtering
--->assembly execution time: 1563.82 sec.

Filtering svtigs
--->remapping svtigs onto the graph using Graphaligner
Error: Graphaligner did not run successfully...
--->Command: GraphAligner -g grch38.t2t.COLO829N1.sv.gfa -f svarp_out/sample_svtigs_tmp.fa -a svarp_out/sample_remap.gaf -t 32 -x vg --precise-clipping 0.970000 --min-alignment-score 5000 --multimap-score-fraction 0.9 > /dev/null 2>&1

I noticed that the Assembly of svtigs seems to output nothing:

❯ tree -s
.
├── [      90284]  sample.log
├── [          0]  sample_remap.gaf
└── [          0]  sample_svtigs_tmp.fa

0 directories, 3 files

Therefore, I want to know if there are some deviations in my steps, if so, please let me know how I can modify it :)

Best wishes,
Wei

Hello,

I would like to use the files available at the following link: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/release/v1.0/final-vcf/final-vcf.phased.vcf.gz.

However, I am having difficulty understanding the notation used for the variant descriptions, specifically: chr1-21837-COMPLEX->s65863s1192-104.

Could you please provide an explanation or direct me to any resources that describe this format in detail?

Thank you very much for your assistance.

Best regards,

Juyoung lee

Hi,

I am trying to use SVarp to detect SV from pangenome graph using this comman line svarp -a sample.gaf -g ref_graph.gfa -f sample.fq.gz -i sample.

ref_graph.gfa was generated by minigraph minigraph -cxggs -t24 T2T-CHM13v2.fasta sample.hap1.fasta sample.hap2.fasta > ref_graph.gfa, alignment was generated by minigraph minigraph -t 24 -cx lr ref_graph.gfa sample.fq.gz > sample_aligned.gaf.

The error message was:

Using wtdbg2 for assembly...
No phase information provided (--phase). SVs will not be phased...

...hallo, merhaba, ola, salaam, hello!!! SVarp is running...

Parameters:
	Minimum read support: 5
	Minimum distance threshold: 100

	Minimum map ratio: 0.9
	Precise clipping (Graphaligner): 0.97
	Alignment score (Graphaligner): 5000


Input files:
	sample_aligned.gaf
	ref_graph.gfa
	sample.fq.gz

Log folder:
	/svarp_log/

Reading the GFA file
Reading the GAF file
Segmentation fault (core dumped)

Can you help me and identify which step I might have gotten wrong?
Thank you!