8000 Sniffles version creating malformed VCF files · Issue #294 · nf-core/nanoseq · GitHub
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Sniffles version creating malformed VCF files #294

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callumjethomas opened this issue Mar 11, 2025 · 1 comment
Open

Sniffles version creating malformed VCF files #294

callumjethomas opened this issue Mar 11, 2025 · 1 comment
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@callumjethomas
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Description of the bug

Sniffles seems to be creating malformed VCF files - this means that sort (SNIFFLES_SORT_VCF) fails with error code 255 and a number of warnings such as:

[W::vcf_parse] Contig 'NC_051849.1STRANDBIAS' is not defined in the header.

Apparently this is a known issue with Sniffles v.1.0.12 that has been resolved with a new version (v2.0.0.2). However nanoseq is currently loading Sniffles v1.0.12. Is it possible to update the Sniffles version to remove this bug?

Command used and terminal output

[W::vcf_parse] Contig 'NC_051849.1STRANDBIAS' is not defined in the header. (Quick workaround: index the file with tabix.)
  [W::vcf_parse_filter] FILTER 'SVMETHOD=Snifflesv1.0.12' is not defined in the header
  [W::vcf_parse_filter] FILTER 'CHR2=NC_051849.1' is not defined in the header
  [W::vcf_parse_filter] FILTER 'END=220562694' is not defined in the header
  [W::vcf_parse_filter] FILTER 'STD_quant_start=0.000000' is not defined in the header
  [W::vcf_parse_filter] FILTER 'STD_quant_stop=0.000000' is not defined in the header
  [W::vcf_parse_filter] FILTER 'Kurtosis_quant_start=3.024139' is not defined in the header
  [W::vcf_parse_filter] FILTER 'Kurtosis_quant_stop=0.817699' is not defined in the header
  [W::vcf_parse_filter] FILTER 'SVTYPE=INV' is not defined in the header
  [W::vcf_parse_filter] FILTER 'SUPTYPE=SR' is not defined in the header
  [W::vcf_parse_filter] FILTER 'SVLEN=219300221' is not defined in the header
  [W::vcf_parse_filter] FILTER 'STRANDS=--' is not defined in the header
  [W::vcf_parse_filter] FILTER 'STRANDS2=0,26,26,0' is not defined in the header
  [E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=STRANDS2=0,26,26,0,Description=\"Dummy\">"
  [E::vcf_parse_filter] Could not add dummy header for FILTER 'STRANDS2=0,26,26,0' at NC_051849.1STRANDBIAS:240
  Error encountered while parsing the input

Relevant files

Example of some of the malformed entries in the VCF file: malformed.vcf.zip

System information

Nextflow version: 24.10.5, build 5935 (04-03-2025 17:55 UTC)
nf-core/nanoseq version: 3.1.0
Profile: singularity
Hardware: HPC
Executor: slurm
@callumjethomas callumjethomas added the bug Something isn't working label Mar 11, 2025
@callumjethomas
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Hopefully this will be fixed by #305?

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