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License: MIT License
Phased structural variant discovery in pangenomes
License: MIT License
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?
--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:
Minigraph-Cactus
to integrate hg38 & chm13 & new-assembly
, and we chose the intermediate graph, which is the output of minigraph.minigraph -cx lr --vc ref.gfa reads.fa.gz > align.gaf
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!
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