[Bug]: sniffles --output-rnames used with duplex reads breaks VCF format

[mp15]

What happened?

1. Fed a duplex BAM file to wf-human-variation for SV calling.
2. wf-human-variation uses sniffles with --output-rnames.
3. sniffles naively outputs the ; from duplex read names into the VCF file
4. filter.sh call to bcftools filter breaks because it thinks the unescaped ;'s separate format fields

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

Docker

Workflow Version

epi2me-labs/wf-human-variation v1.5.2-gac6fdb9

Relevant log output

ERROR ~ Error executing process > 'sv:variantCall:filterCalls (1)'

Caused by:
  Process `sv:variantCall:filterCalls (1)` terminated with an error exit status (8)

Command executed:

  get_filter_calls_command.py         --target_bedfile allChromosomes.bed         --vcf WTSI-OESO_152.sniffles.vcf         --depth_summary WTSI-OESO_152.mosdepth.summary.txt         --min_sv_length 30         --max_sv_length 100000         --sv_types DEL INS         --min_read_support auto         --min_read_support_limit 2 > filter.sh

  bash filter.sh > WTSI-OESO_152.filtered.vcf

Command exit status:
  8

Command output:
  (empty)

Command error:
  [W::vcf_parse_info] INFO 'f2e03f85-bf08-473c-bc65-6f72274efc9e,5504d8a2-edc5-4a16-8d3e-95b5860cf0c8,2de90ca1-c356-44ea-ae12-edfd388dd13e,e3ee18fe-ef87-4fcd-a053-36a3b024882f,7f8bc40d-2fad-415c-8390-a333c648042e,5b04693c-badd-4ec8-9d26-8669e2519491' is not defined in the header, assuming Type=String
  [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=<ID=f2e03f85-bf08-473c-bc65-6f72274efc9e,5504d8a2-edc5-4a16-8d3e-95b5860cf0c8,2de90ca1-c356-44ea-ae12-edfd388dd13e,e3ee18fe-ef87-4fcd-a053-36a3b024882f,7f8bc40d-2fad-415c-8390-a333c648042e,5b04693c-badd-4ec8-9d26-8669e2519491,Number=1,Type=String,Description=\"Dummy\">"
  [E::vcf_parse_info] Could not add dummy header for INFO 'f2e03f85-bf08-473c-bc65-6f72274efc9e,5504d8a2-edc5-4a16-8d3e-95b5860cf0c8,2de90ca1-c356-44ea-ae12-edfd388dd13e,e3ee18fe-ef87-4fcd-a053-36a3b024882f,7f8bc40d-2fad-415c-8390-a333c648042e,5b04693c-badd-4ec8-9d26-8669e2519491' at chr1:10890
  Error: VCF parse error

Work dir:
  /fastdata/152s_nextflow_workspace/bf/94d43191f236319b49989c1bfabbfa

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

bad VCF output:

chr1    10890   Sniffles2.INS.5S0       N       AGGGGAGGAGGCGTGGCACAGGCGCAGAGACACATGCTAGCGCGCCCAAGCT    55      PASS    IMPRECISE;SVTYPE=INS;SVLEN=114;END=10890;SUPPORT=26;RNAMES=1c2f71d2-8b13-483f-ad24-942b9c410169,e3ee18fe-ef87-4fcd-a053-36a3b024882f;f2e03f85-bf08-473c-bc65-6f72274efc9e,5504d8a2-edc5-4a16-8d3e-95b5860cf0c8,2de90ca1-c356-44ea-ae12-edfd388dd13e,e3ee18fe-ef87-4fcd-a053-36a3b024882f,7f8bc40d-2fad-415c-8390-a333c648042e,5b04693c-badd-4ec8-9d26-8669e2519491;3fe23644-d40d-411c-aa94-aa435a85de77,07fce883-3ee1-4c2b-b3ae-65ffa103e636,4491b600-cf70-46e3-9ed8-9cc762fa4db9,5e4af17b-7350-407e-93e4-06d085debf18,5b04693c-badd-4ec8-9d26-8669e2519491,da7a369a-fc62-4d60-973c-d3cfe1150dbc,a74d74e2-c0c8-486a-9008-c2bc50a4d486,d2ee0a97-b591-4d7d-bc06-30101c1a612d,11a960ac-1f68-4728-818c-b077db8629db,0f4acfdb-3a41-479a-a8aa-3150f58efc76,6cdaba7d-a875-428a-bd79-5cac2b470b23,f2e03f85-bf08-473c-bc65-6f72274efc9e,b9b8d226-f12e-48f4-a983-60ca4c49c4d8,5666350b-b9c5-4586-967a-4cbcd10cfc09,2e750ddf-bea6-4a4c-99b9-cdebb8c7976a,3c3dd0df-5e17-44d5-bff1-4dc489126539;0f4acfdb-3a41-479a-a8aa-3150f58efc76,3fe23644-d40d-411c-aa94-aa435a85de77,3c3dd0df-5e17-44d5-bff1-4dc489126539,e96248ee-8981-4d7c-b99a-5f27cc67cb5a,5831ceba-ef36-4285-bb28-0aec8a20fab7;COVERAGE=36,36,36,36,36;STRAND=+-;AF=0.722;STDEV_LEN=27.522;STDEV_POS=54.939;SUPPORT_LONG=0 GT:GQ:DR:DV     0/1:27:10:26

[mp15]

Bug logged against sniffles fritzsedlazeck/Sniffles#403

[SamStudio8]

This seems to have gone a bit stale upstream but I'll leave the issue open to track the problem.

[flokraft85]

Hi,
I have the same issue. Is there inbetween a fix for duplex bams avaiable?

Best,
Florian