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Dear,
Dose the svimmer generate SVs that can be detected by all softerwares ( intersection of SVs from different softewares), or merge all SVs of different files (union of SVs from different softewares)?
Many thanks!

Dear developers.
When I use svimmer to merge the vcf created by manta. I found some warnings in the log file.

[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?

This is probably due to the position becoming from 0 after converting the INV variant type with the convertInversion.py script supported by manta.

Here is an example created by manta (diploidSV.vcf.gz)

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE1
 1       1       MantaBND:82572:0:1:0:0:0:0      G       [1:5440[G       279     PASS    SVTYPE=BND;MATEID=MantaBND:82572:0:1:0:0:0:1;CIPOS=0,2;HOMLEN=2;HOMSEQ=CT;BND_DEPTH=12;MATE_BND_DEPTH=14
 1       5438    MantaBND:82572:0:1:0:0:0:1      G       [1:3[G  279     PASS    SVTYPE=BND;MATEID=MantaBND:82572:0:1:0:0:0:0;CIPOS=0,2;HOMLEN=2;HOMSEQ=CA;BND_DEPTH=14;MATE_BND_DEPTH=12

After converting, the position changed to 0:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE1
  1       0       MantaINV:82572:0:1:0:0:0                <INV>   279     PASS    END=5439;SVTYPE=INV;SVLEN=5439;CIPOS=0,2;CIEND=-2,0;HOMLEN=2;HOMSEQ=GC;INV5     GT:FT:GQ:PL:PR:SR

This result may caused "[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?"
Does this warning have a bad effect on the merged.vcf.gz results?

Hi,

I am trying to merge a list of VCFs of SVs using svimmer, but receive the following error:

Traceback (most recent call last): File "../../../svimmer/svimmer", line 140, in <module> header = read_header(vcf_f) # Read the header of the first VCF file File "../../../svimmer/svimmer", line 32, in read_header line = vcf_f.readline().decode("utf-8") AttributeError: 'str' object has no attribute 'decode'

Thanks

Dear Hannes,

First of all, thank you for writing and maintaining such great resources as graphtyper and svimmer!

I have noticed that svimmer writes warnings into STDOUT, messing up piping into bgzip / a VCF file if no variant is present for one of the chromosomes in one of the input VCF files. This is only a minor complication as warnings could be grepped out before bgzip.

Nevertheless, it would be nicer to stream into STDERR instead, by adjusting line 77 to:
print("Warning: Contig '%s' was not found in file %s!" % (chrom, vcf_filename.rstrip("\n")), file=sys.stderr)

Thanks and best,
David

Dear author,
Some of my vcf files can only generate csi index and cannot generate tbi index due to the length of chromosome, so I would like to ask if you can optimize the code to support csi index

Hi Hannes,

I am trying to merge SV calls from marsupial chromosomes. Some of these are >> 512 Mb in length, and hence need to be indexed via tabix -C -p vcf. This doesn't create a .tbi index, but a .csi one instead (a bit more explanation here).

However, svimmer currently relies on .tbi inputs only - could you possibly at .csi support? Happy to provide you with log files & tests if this helps.

Many thanks,
Max

Hi，

I found the SVTYPE for duplication annotated by three differet types in SVIM VCF: "DUP", "DUP:TANDEM", "DUP:INT". Maybe I need add info_dict["SVTYPE"] == "DUP:TANDEM" or info_dict["SVTYPE"] == "DUP:INT" to the following part highlighted by italic. Also, from the following codes, why did you treat the INV as the INS?
Join related SV types
if "SVTYPE" in info_dict:
if info_dict["SVTYPE"] == "DEL_ALU" or info_dict["SVTYPE"] == "DEL_LINE1":
info_dict["SVTYPE"] = "DEL"
elif info_dict["SVTYPE"] == "ALU" or info_dict["SVTYPE"] == "LINE1" or info_dict["SVTYPE"] == "SVA" or
info_dict["SVTYPE"] == "DUP" or info_dict["SVTYPE"] == "CNV" or info_dict["SVTYPE"] == "INVDUP" or
info_dict["SVTYPE"] == "INV":
info_dict["SVTYPE"] = "INS"
elif info_dict["SVTYPE"] == "TRA":
info_dict["SVTYPE"] = "BND"

Sincerely,
Zheng Zhuqing

i merge vcf by using svimmer, but the the format of DEL is strange, the REF is G while ALT is

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr1    10649859        .       G       <DEL>   0       .       END=10653389;SVTYPE=DEL

but I want to gained the normal format with DEL， for example：

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr1    10649859        .      GTGTCTCATGTCCGCGTCCCGTGTCTC.....  G          0       .       END=10653389;SVTYPE=DEL

the REF is GTGTCTCATGTCCGCGTCCCGTGTCTC..... while ALT is G,how to gain it,thanks~

Dear @hannespetur

Thank you and colleagues for the very nice svimmer and graphtyper software.

I would like to use svimmer and graphtyper for forced genotyping of the UNION of Manta ( many WGS) and SVIM-ASM (few assembly) discovered SVs in many WGS samples.

SVIM-ASM github
https://github.com/eldariont/svim-asm

The versions that I am using are svimmer/20211209 and graphtyper/2.7.3

When I try to get the (merged) UNION of SVs via svimmer I get this error.

Traceback (most recent call last):
  File "/tools/eb/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/tools/eb/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/multiprocessing/pool.py", line 51, in starmapstar
    return list(itertools.starmap(args[0], args[1]))
  File "/tools/eb/software/svimmer/20211209-GCC-10.2.0/svimmer", line 82, in append_svs_from_vcf
    svs.append(SV(record, check_type=not args.ignore_types, join_mode=args.join_mode, output_ids=args.ids))
  File "/tools/eb/software/svimmer/20211209-GCC-10.2.0/sv.py", line 75, in __init__
    assert False
AssertionError

This is caused by svimmer not recognizing the DUP:TANDEM and DUP:INT types that SVIM-ASM outputs.

I can use the svimmer argument --ignore-types to get svimmer to work.
But then graphtyper complains about Unknown SV type and I guess also drops the SVs of unknown type??

<warning> constructor.cpp:106 Unknown SV type DUP:TANDEM
<warning> constructor.cpp:106 Unknown SV type DUP:TANDEM

Would it be possible to add a mapping for DUP:TANDEM and DUP:INT in the main branch of the svimmer code here?

Then the the combination of SVIM-ASM and svimmer/graphtyper would work for me and others with the same use case/combination of tools.

I also don't understand why SVs of type DUP, CNV and INV are mapped to type INS here

That does not make sense to me. INS is a novel sequence , DUP, CNV and INV are sequences already found on the reference genome and therefore also need to genotyped differently in graphtyper?

Also what I find strange is that both svimmer and graphtyper do output SVs of type DUP.
That I can't square with the mapping of DUP, CNV and INV to INS. Or maybe the SV type is re-calculated again somewhere else in svimmer/graphtyper?

Thank you for your thoughts and help on this.

@hannespetur

Just a couple questions on join-mode...

What is the difference between the two join-modes? When should the non-default join-mode be used (eg: join_mode=false)?

Is the output different or is it related to some optimizing of the run-time?

--join-mode",
dest="join_mode",
action="store_true",
help="""Set if the merging should join VCFs from the first file to the other files."""