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Error when working with --ins-info-key
#78
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Apparently the info field describing ##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"> |
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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:The command run is:
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
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