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atks
"bcf_fmt_array" error
Hi
I am using vt decompose -s -d on a VCF file and encountered an "Unexpected type 0" error without produced the resulting VCF
decompose v0.5
options: input VCF file test.vcf
[s] smart decomposition true (experimental)
[o] output VCF file -
1:1168012:CCTG/C
1:1226941:CCG/C
1:1273245:GCTGGGGGTGGAGCAGCAGCGGGGTGGGGTGGAA/G
1:1323901:AAAAAC/A
1:1564778:G/T
1:2704224:TC/T
1:2704227:AGCT/A
[E::bcf_fmt_array] Unexpected type 0
Below is the VCF
1 1168012 . CCTG C . germline;slippage;weak_evidence CONTQ=17;DP=31;ECNT=1;GERMQ=1;MBQ=20,20;MFRL=155,174;MMQ=60,60;MPOS=42;NALOD=1.000;NLOD=2.71;POPAF=5.40;ROQ=93;RPA=4,3;RU=CTG;SEQQ=1;STR;STRANDQ=60;STRQ=1;TLOD=6.90 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:17,0:0.091:17:8,0:8,0:9,8,0,0 0/1:8,3:0.299:11:1,0:5,3:5,3,2,1
1 1226941 . CCG C . contamination;weak_evidence CONTQ=3;DP=66;ECNT=1;GERMQ=75;MBQ=20,20;MFRL=157,138;MMQ=60,60;MPOS=15;NALOD=1.27;NLOD=5.11;POPAF=5.40;ROQ=93;SEQQ=1;STRANDQ=29;TLOD=3.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:32,0:0.051:32:16,0:16,0:15,17,0,0 0/1:29,2:0.104:31:12,2:16,0:13,16,1,1
1 1273245 . GCTGGGGGTGGAGCAGCAGCGGGGTGGGGTGGAA G . contamination;normal_artifact;weak_evidence CONTQ=1;DP=176;ECNT=1;GERMQ=93;MBQ=34,20;MFRL=157,140;MMQ=60,60;MPOS=37;NALOD=-3.576e+00;NLOD=4.71;POPAF=2.58;ROQ=93;SEQQ=1;STRANDQ=93;TLOD=3.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:53,2:0.041:55:19,0:26,2:41,12,1,1 0/1:75,2:0.032:77:27,0:36,2:56,19,1,1
1 1323901 . AAAAAC A . contamination;slippage;weak_evidence CONTQ=1;DP=94;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=152,188;MMQ=60,60;MPOS=59;NALOD=1.21;NLOD=4.50;POPAF=5.40;ROQ=93;RPA=3,2;RU=AAAAC;SEQQ=1;STR;STRANDQ=93;STRQ=1;TLOD=5.94 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:26,0:0.058:26:19,0:6,0:12,14,0,0 0/1:58,2:0.057:60:20,0:35,2:30,28,1,1
1 1564778 . G T . orientation;weak_evidence CONTQ=20;DP=37;ECNT=1;GERMQ=39;MBQ=20,20;MFRL=150,158;MMQ=60,60;MPOS=44;NALOD=1.11;NLOD=3.61;POPAF=5.40;ROQ=1;SEQQ=1;STRANDQ=30;TLOD=3.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:23,0:0.071:23:10,0:13,0:12,11,0,0 0/1:12,2:0.222:14:12,2:0,0:6,6,1,1
1 2704224 . TC T . contamination;haplotype;weak_evidence CONTQ=1;DP=93;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=155,138;MMQ=60,60;MPOS=48;NALOD=1.26;NLOD=5.10;POPAF=5.40;ROQ=93;RPA=2,1;RU=C;SEQQ=1;STR;STRANDQ=24;STRQ=93;TLOD=5.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:31,0:0.052:31:20,0:11,0:0|1:2704224_TC_T:2704224:14,17,0,0 0|1:56,2:0.058:58:32,2:24,0:0|1:2704224_TC_T:2704224:25,31,1,1
1 2704227 . AGCT A . contamination;haplotype;weak_evidence CONTQ=1;DP=90;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=155,138;MMQ=60,60;MPOS=-2147483648;NALOD=1.26;NLOD=5.12;POPAF=5.40;ROQ=93;SEQQ=1;STRANDQ=34;TLOD=5.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:31,0:0.053:31:20,0:11,0:0|1:2704224_TC_T:2704224:14,17,0,0 0|1:56,2:0.059:58:32,2:23,0:0|1:2704224_TC_T:2704224:25,31,1,1
1 3645985 . GGCA G . contamination;slippage;weak_evidence CONTQ=1;DP=243;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=156,172;MMQ=60,60;MPOS=68;NALOD=1.77;NLOD=16.81;POPAF=5.40;ROQ=93;RPA=4,3;RU=GCA;SEQQ=1;STR;STRANDQ=57;STRQ=1;TLOD=6.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:97,0:0.017:97:40,0:57,0:42,55,0,0 0/1:116,4:0.044:120:53,2:60,2:54,62,2,2
@ycl6
Can you add the headers of the VCF file or link a small VCF where the error can be reproduced?
On Nov 13, 2019, at 4:02 PM, I-Hsuan Lin [email protected] wrote:
Hi
I am using vt decompose -s -d on a VCF file and encountered an "Unexpected type 0" error without produced the resulting VCF
decompose v0.5
options: input VCF file test.vcf [s] smart decomposition true (experimental) [o] output VCF file -
1:1168012:CCTG/C 1:1226941:CCG/C 1:1273245:GCTGGGGGTGGAGCAGCAGCGGGGTGGGGTGGAA/G 1:1323901:AAAAAC/A 1:1564778:G/T 1:2704224:TC/T 1:2704227:AGCT/A [E::bcf_fmt_array] Unexpected type 0 Below is the VCF
1 1168012 . CCTG C . germline;slippage;weak_evidence CONTQ=17;DP=31;ECNT=1;GERMQ=1;MBQ=20,20;MFRL=155,174;MMQ=60,60;MPOS=42;NALOD=1.000;NLOD=2.71;POPAF=5.40;ROQ=93;RPA=4,3;RU=CTG;SEQQ=1;STR;STRANDQ=60;STRQ=1;TLOD=6.90 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:17,0:0.091:17:8,0:8,0:9,8,0,0 0/1:8,3:0.299:11:1,0:5,3:5,3,2,1 1 1226941 . CCG C . contamination;weak_evidence CONTQ=3;DP=66;ECNT=1;GERMQ=75;MBQ=20,20;MFRL=157,138;MMQ=60,60;MPOS=15;NALOD=1.27;NLOD=5.11;POPAF=5.40;ROQ=93;SEQQ=1;STRANDQ=29;TLOD=3.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:32,0:0.051:32:16,0:16,0:15,17,0,0 0/1:29,2:0.104:31:12,2:16,0:13,16,1,1 1 1273245 . GCTGGGGGTGGAGCAGCAGCGGGGTGGGGTGGAA G . contamination;normal_artifact;weak_evidence CONTQ=1;DP=176;ECNT=1;GERMQ=93;MBQ=34,20;MFRL=157,140;MMQ=60,60;MPOS=37;NALOD=-3.576e+00;NLOD=4.71;POPAF=2.58;ROQ=93;SEQQ=1;STRANDQ=93;TLOD=3.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:53,2:0.041:55:19,0:26,2:41,12,1,1 0/1:75,2:0.032:77:27,0:36,2:56,19,1,1 1 1323901 . AAAAAC A . contamination;slippage;weak_evidence CONTQ=1;DP=94;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=152,188;MMQ=60,60;MPOS=59;NALOD=1.21;NLOD=4.50;POPAF=5.40;ROQ=93;RPA=3,2;RU=AAAAC;SEQQ=1;STR;STRANDQ=93;STRQ=1;TLOD=5.94 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:26,0:0.058:26:19,0:6,0:12,14,0,0 0/1:58,2:0.057:60:20,0:35,2:30,28,1,1 1 1564778 . G T . orientation;weak_evidence CONTQ=20;DP=37;ECNT=1;GERMQ=39;MBQ=20,20;MFRL=150,158;MMQ=60,60;MPOS=44;NALOD=1.11;NLOD=3.61;POPAF=5.40;ROQ=1;SEQQ=1;STRANDQ=30;TLOD=3.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:23,0:0.071:23:10,0:13,0:12,11,0,0 0/1:12,2:0.222:14:12,2:0,0:6,6,1,1 1 2704224 . TC T . contamination;haplotype;weak_evidence CONTQ=1;DP=93;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=155,138;MMQ=60,60;MPOS=48;NALOD=1.26;NLOD=5.10;POPAF=5.40;ROQ=93;RPA=2,1;RU=C;SEQQ=1;STR;STRANDQ=24;STRQ=93;TLOD=5.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:31,0:0.052:31:20,0:11,0:0|1:2704224_TC_T:2704224:14,17,0,0 0|1:56,2:0.058:58:32,2:24,0:0|1:2704224_TC_T:2704224:25,31,1,1 1 2704227 . AGCT A . contamination;haplotype;weak_evidence CONTQ=1;DP=90;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=155,138;MMQ=60,60;MPOS=-2147483648;NALOD=1.26;NLOD=5.12;POPAF=5.40;ROQ=93;SEQQ=1;STRANDQ=34;TLOD=5.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:31,0:0.053:31:20,0:11,0:0|1:2704224_TC_T:2704224:14,17,0,0 0|1:56,2:0.059:58:32,2:23,0:0|1:2704224_TC_T:2704224:25,31,1,1 1 3645985 . GGCA G . contamination;slippage;weak_evidence CONTQ=1;DP=243;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=156,172;MMQ=60,60;MPOS=68;NALOD=1.77;NLOD=16.81;POPAF=5.40;ROQ=93;RPA=4,3;RU=GCA;SEQQ=1;STR;STRANDQ=57;STRQ=1;TLOD=6.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:97,0:0.017:97:40,0:57,0:42,55,0,0 0/1:116,4:0.044:120:53,2:60,2:54,62,2,2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.
@atks
I put the first couple of lines of the VCF at pastebin. https://pastebin.com/raw/f46eh1K4
With the content named "test1.vcf"
vt decompose -s -d test1.vcf > test2.vcf
I will get
decompose v0.5
options: input VCF file test1.vcf
[s] smart decomposition true (experimental)
[o] output VCF file -
1:1168012:CCTG/C
1:1226941:CCG/C
1:1273245:GCTGGGGGTGGAGCAGCAGCGGGGTGGGGTGGAA/G
1:1323901:AAAAAC/A
1:1564778:G/T
1:2704224:TC/T
1:2704227:AGCT/A
[E::bcf_fmt_array] Unexpected type 0
@atks Thanks. I will report another issue probably is related.
I run bcftools on same test1.vcf to do decompose and normalize without error
bcftools norm --multiallelics -any -f human_g1k_v37_decoy.fasta test1.vcf > test2.vcf
Lines total/split/realigned/skipped: 15/2/4/0
I then run vt sort test2.vcf and received [E:bcf_synced_reader.h:108 operator()] alleles not defined in VCF record. error
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 005N 005T
1 1168012 . CCTG C . germline;slippage;weak_evidence CONTQ=17;DP=31;ECNT=1;GERMQ=1;MBQ=20,20;MFRL=155,174;MMQ=60,60;MPOS=42;NALOD=1;NLOD=2.71;POPAF=5.4;ROQ=93;RPA=4,3;RU=CTG;SEQQ=1;STR;STRANDQ=60;STRQ=1;TLOD=6.9 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:17,0:0.091:17:8,0:8,0:9,8,0,0 0/1:8,3:0.299:11:1,0:5,3:5,3,2,1
1 1226941 . CCG C . contamination;weak_evidence CONTQ=3;DP=66;ECNT=1;GERMQ=75;MBQ=20,20;MFRL=157,138;MMQ=60,60;MPOS=15;NALOD=1.27;NLOD=5.11;POPAF=5.4;ROQ=93;SEQQ=1;STRANDQ=29;TLOD=3.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:32,0:0.051:32:16,0:16,0:15,17,0,0 0/1:29,2:0.104:31:12,2:16,0:13,16,1,1
1 1273245 . GCTGGGGGTGGAGCAGCAGCGGGGTGGGGTGGAA G . contamination;normal_artifact;weak_evidence CONTQ=1;DP=176;ECNT=1;GERMQ=93;MBQ=34,20;MFRL=157,140;MMQ=60,60;MPOS=37;NALOD=-3.576;NLOD=4.71;POPAF=2.58;ROQ=93;SEQQ=1;STRANDQ=93;TLOD=3.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:53,2:0.041:55:19,0:26,2:41,12,1,1 0/1:75,2:0.032:77:27,0:36,2:56,19,1,1
1 1323901 . AAAAAC A . contamination;slippage;weak_evidence CONTQ=1;DP=94;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=152,188;MMQ=60,60;MPOS=59;NALOD=1.21;NLOD=4.5;POPAF=5.4;ROQ=93;RPA=3,2;RU=AAAAC;SEQQ=1;STR;STRANDQ=93;STRQ=1;TLOD=5.94 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:26,0:0.058:26:19,0:6,0:12,14,0,0 0/1:58,2:0.057:60:20,0:35,2:30,28,1,1
1 1564778 . G T . orientation;weak_evidence CONTQ=20;DP=37;ECNT=1;GERMQ=39;MBQ=20,20;MFRL=150,158;MMQ=60,60;MPOS=44;NALOD=1.11;NLOD=3.61;POPAF=5.4;ROQ=1;SEQQ=1;STRANDQ=30;TLOD=3.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:23,0:0.071:23:10,0:13,0:12,11,0,0 0/1:12,2:0.222:14:12,2:0,0:6,6,1,1
1 2704224 . TC T . contamination;haplotype;weak_evidence CONTQ=1;DP=93;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=155,138;MMQ=60,60;MPOS=48;NALOD=1.26;NLOD=5.1;POPAF=5.4;ROQ=93;RPA=2,1;RU=C;SEQQ=1;STR;STRANDQ=24;STRQ=93;TLOD=5.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|0:31,0:0.052:31:20,0:11,0:0|1:2704224_TC_T:2704224:14,17,0,0 0|1:56,2:0.058:58:32,2:24,0:0|1:2704224_TC_T:2704224:25,31,1,1
1 2704227 . AGCT A . contamination;haplotype;weak_evidence CONTQ=1;DP=90;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=155,138;MMQ=60,60;MPOS=.;NALOD=1.2[E:bcf_synced_reader.h:108 operator()] alleles not defined in VCF record.
Hi, has any progress been made with this? I am seeing the same error [E::bcf_fmt_array] Unexpected type 0. Is it from the ECNT INFO field?
Reason I suspect this is because the output terminates right at the recalculation for the decomposed record at ECNT (with no debug flag, output to stdout):
chr1 22447102 . CAA C . PASS CONTQ=66;DP=99;ECNT=1;GERMQ=81;MBQ=30,30;MFRL=344,344;MMQ=60,60;MPOS=18;NALOD=0.737;NLOD=4.15;POPAF=2.75;ROQ=93;RPA=16,14,15;RU=A;SEQQ=59;STR;STRANDQ=78;STRQ=93;TLOD=11.39;OLD_MULTIALLELIC=chr1:22447102:CAA/C/CA GT:AD:AF:DP:F1R2:F2R1:SB 0/0:13,0:0.048:16:8,0:5,0:5,8,1,2 0/1/.:52,7:0.117:64:18,3:26,4:14,38,8,4
chr1 22447102 . CAA CA . PASS CONTQ=66;DP=99;ECNT=[E::bcf_fmt_array] Unexpected type 0
then, running with the debug flag vt decompose -s -d:
chr1 22447102 . CAA C . PASS CONTQ=66;DP=99;ECNT=1;GERMQ=81;MBQ=30,30;MFRL=344,344;MMQ=60,60;MPOS=18;NALOD=0.737;NLOD=4.15;POPAF=2.75;ROQ=93;RPA=16,14,15;RU=A;SEQQ=59;STR;STRANDQ=78;STRQ=93;TLOD=11.39;OLD_MULTIALLELIC=chr1:22447102:CAA/C/CA GT:AD:AF:DP:F1R2:F2R1:SB 0/0:13,0:0.048:16:8,0:5,0:5,8,1,2 0/1/.:52,7:0.117:64:18,3:26,4:14,38,8,4
chr1 22447102 . CAA CA . PASS CONTQ=66;DP=99;ECNT=chr1:23142704:C/T
I'm not sure if this helps any troubleshooting. I can also provide a sample VCF
