Error when working with --ins-info-key

[nvnieuwk]

Hi, I'm trying to run Paragraph on VCFs that have been merged from different callers. Therefore I had to create a uniform info field for all callers which I called SVINSSEQ (which is the one from manta). When I try to run the tool specifying this key, it somehow turns the sequence into a tuple which causes the following error:

  Traceback (most recent call last):
    File "/usr/local/lib/python3.7/multiprocessing/pool.py", line 121, in worker
      result = (True, func(*args, **kwds))
    File "/usr/local/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
      return list(map(*args))
    File "/usr/local/lib/python3/grm/vcf2paragraph/__init__.py", line 286, in run_vcf2paragraph
      alt_paths=params["alt_paths"])
    File "/usr/local/lib/python3/grm/vcf2paragraph/__init__.py", line 86, in convert_vcf
      ref, indexed_vcf.name, ins_info_key, chrom, start, end, ref_node_padding, allele_graph)
    File "/usr/local/lib/python3/grm/vcfgraph/vcfgraph.py", line 128, in create_from_vcf
      graph.add_record(record, allele_graph, varId, ins_info_key)
    File "/usr/local/lib/python3/grm/vcfgraph/vcfgraph.py", line 179, in add_record
      ins_seq = vcf.info[ins_info_key].upper()
  AttributeError: 'tuple' object has no attribute 'upper'

The command run is:

multigrmpy.py \
    --input PosCon4.vcf.gz \
    --manifest PosCon4.tsv \
    --output PosCon4_genotyped \
    --reference GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna \
    --threads 1 \
    --ins-info-key SVINSSEQ

The VCF contains one variant (insertion) which looks like this:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PosCon4
chrX	153903418	1_INS00000000	T	<INS>	480	PASS	PRECISE;SVTYPE=INS;SVMETHOD=JASMINE;END=153903418;SVLEN=35;PE=0;MAPQ=0;CT=NtoN;CIPOS=-14,14;CIEND=-14,14;SRMAPQ=60;INSLEN=35;HOMLEN=13;SR=8;SRQ=1;SVINSSEQ=AAGATGCGGGGTGTGATGTGCACCTGTGTGTGCTGCGGGTGTGTGCGTGTGTGGTGTTGGCTGTGCGTATGTGGTGTGGTATGGTGTGCAGGTGCATGCAGGTGCGTGGTGTGTATGGCTGTGTGGTGGGTACATGTGTGGGTGTGTGGCGTATGGGAGTGTGTGATGTGTGCATGTGTGTGGTGTG;CE=1.66556;STARTVARIANCE=0.000000;ENDVARIANCE=0.000000;AVG_LEN=35.000000;AVG_START=153903418.000000;AVG_END=153903419.000000;VARCALLS=1;ALLVARS_EXT=(INS00000000);SUPP_VEC_EXT=010;IDLIST_EXT=INS00000000;SUPP_EXT=1;SUPP_VEC=010;SUPP=1;IDLIST=INS00000000;INTRASAMPLE_IDLIST=INS00000000	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	1/1:-125.994,-10.8314,0:108:PASS:12619:21001:8382:2:0:0:0:36

(headers were removed here to not make this too long)

What can I do to solve this?
Many thanks in advance
-Nicolas

[nvnieuwk]

Apparently the info field describing SVINSSEQ should look like this:

##INFO=<ID=SVINSSEQ,Number=1,Type=String,Description="Sequence of insertion">

And the error happens when the header looks like this:

##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">