You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am trying to annotate a project .vcf file retrieved from GLnexus with OpenCRAVAT.
the .bcf file file gets converted to an .vcf file with: bcftools view <bcf_file> | bgzip -c > pvcf_all_glnexus.vcf.gz
oc is installed with conda install open-cravat==2.2.1.
if I run this file with oc run -l hg38 -t csv -x pvcf_all_glnexus.vcf.gz
for most of the lines it works perfectly but for some I get the following errors in the err log for multiple lines:
SOURCE:error.converter
LINE:530
INPUT:1 925408 1_925408_TTGGCGCCTGC_T TTGGCGCCTGC T 20 MONOALLELIC AF=0.1;AQ=20 GT:DP:AD:GQ:PL:RNC ./.:0:.,0:1:0,0,0:11 ./.:0:.,0:1:0,0,0:11 ./.:0:.,0:0:0,0,0:II ./1:2:.,2:3:0,0,0:1. ./.:3:.,0:7:0,0,0:11 ./.:5:.,0:13:0,0,0:11 ./.:5:.,0:12:0,0,0:11 ./.:0:.,0:0:0,0,0:II ./.:4:.,0:9:0,0,0:11 ./.:0:.,0:0:0,0,0:II
ERROR:unsupported operand type(s) for +: 'int' and 'NoneType'
#
SOURCE:error.converter
LINE:705
INPUT:1 976745 1_976745_CG_C CG C 17 . AF=0.5;AQ=17 GT:DP:AD:GQ:PL:RNC ./.:13:.:.:0,0,0:OO ./1:20:.,8:.:0,0,0:O. 1/1:19:3,15:10:13,15,0:.. 1/1:23:2,20:12:15,22,0:.. 1/1:20:0,18:14:17,35,0:.. ./.:10:.:.:0,0,0:OO 1/1:31:4,24:2:5,13,0:.. ./1:8:.,4:.:0,0,0:O. ./.:21:15,4:7:0,5,21:II ./.:17:14,3:4:0,1,14:II
ERROR:unsupported operand type(s) for +: 'int' and 'NoneType'
the subset of the input .vcf file looks like this (2. and 5. line are problematic, one line before and after the error is included for comparison) :
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##GLnexusVersion=v1.2.7-0-g0e74fc4
##GLnexusConfigName=DeepVariant
##GLnexusConfigCRC32C=2857227159
##GLnexusConfig={unifier_config: {drop_filtered: false, min_allele_copy_number: 1, min_AQ1: 10, min_AQ2: 10, min_GQ: 0, max_alleles_per_site: 32, monoallelic_sites_for_lost_alleles: true, preference: common}, genotyper_config: {revise_genotypes: true, min_assumed_allele_frequency: 9.99999975e-05, required_dp: 0, allow_partial_data: true, allele_dp_format: AD, ref_dp_format: MIN_DP, output_residuals: false, more_PL: true, squeeze: false, trim_uncalled_alleles: true, output_format: BCF, liftover_fields: [{orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}, {orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}, {orig_names: [GQ], name: GQ, description: "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}, {orig_names: [PL], name: PL, description: "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred-scaled genotype Likelihoods\">", type: int, number: genotype, default_type: missing, count: 0, combi_method: missing, ignore_non_variants: true}]}}
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency estimate for each alternate allele">
##INFO=<ID=AQ,Number=A,Type=Integer,Description="Allele Quality score reflecting evidence for each alternate allele (Phred scale)">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##FILTER=<ID=MONOALLELIC,Description="Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=RNC,Number=2,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, I = gVCF input site is non-called, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present, 1 = site is Monoallelic, no assertion about presence of REF or ALT allele">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype Likelihoods">
##contig=<ID=1,length=248956422>
##contig=<ID=10,length=133797422>
##contig=<ID=11,length=135086622>
##contig=<ID=12,length=133275309>
##contig=<ID=13,length=114364328>
##contig=<ID=14,length=107043718>
##contig=<ID=15,length=101991189>
##contig=<ID=16,length=90338345>
##contig=<ID=17,length=83257441>
##contig=<ID=18,length=80373285>
##contig=<ID=19,length=58617616>
##contig=<ID=2,length=242193529>
##contig=<ID=20,length=64444167>
##contig=<ID=21,length=46709983>
##contig=<ID=22,length=50818468>
##contig=<ID=3,length=198295559>
##contig=<ID=4,length=190214555>
##contig=<ID=5,length=181538259>
##contig=<ID=6,length=170805979>
##contig=<ID=7,length=159345973>
##contig=<ID=8,length=145138636>
##contig=<ID=9,length=138394717>
##contig=<ID=MT,length=16569>
##contig=<ID=X,length=156040895>
##contig=<ID=Y,length=57227415>
##bcftools_viewVersion=1.11+htslib-1.11
##bcftools_viewCommand=view pvcf_all_glnexus.bcf; Date=Thu Jan 14 22:27:57 2021
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_1 sample_2 sample_3 sample_4 sample_5 sample_6 sample_7 sample_8 sample_9 sample_10
1 925408 1_925408_TTGG_T TTGG T 36 . AF=0.4;AQ=36 GT:DP:AD:GQ:PL:RNC 0/0:0:0,0:1:0,3,29:.. 0/0:0:0,0:1:0,3,29:.. ./.:0:0,0:0:0,0,0:II ./.:2:0,0:7:0,0,0:-- 1/1:3:0,3:3:25,7,0:.. 1/1:5:0,5:9:32,13,0:.. 1/1:5:0,5:9:34,13,0:.. ./.:0:0,0:0:0,0,0:II 1/1:4:0,4:8:36,12,0:.. ./.:0:0,0:0:0,0,0:II
1 925408 1_925408_TTGGCGCCTGC_T TTGGCGCCTGC T 20 MONOALLELIC AF=0.1;AQ=20 GT:DP:AD:GQ:PL:RNC ./.:0:.,0:1:0,0,0:11 ./.:0:.,0:1:0,0,0:11 ./.:0:.,0:0:0,0,0:II ./1:2:.,2:3:0,0,0:1. ./.:3:.,0:7:0,0,0:11 ./.:5:.,0:13:0,0,0:11 ./.:5:.,0:12:0,0,0:11 ./.:0:.,0:0:0,0,0:II ./.:4:.,0:9:0,0,0:11 ./.:0:.,0:0:0,0,0:II
1 925412 1_925412_CGCCTGCG_C CGCCTGCG C 32 . AF=0.4;AQ=32 GT:DP:AD:GQ:PL:RNC 0/0:0:0,0:1:0,3,29:.. 0/0:0:0,0:1:0,3,29:.. ./.:0:0,0:0:0,0,0:II ./.:2:.:.:0,0,0:UU 1/1:3:0,3:3:24,7,0:.. 1/1:5:0,5:9:30,13,0:.. 1/1:5:0,5:8:32,12,0:.. ./.:0:0,0:0:0,0,0:II 1/1:4:0,4:5:31,9,0:.. ./.:0:0,0:0:0,3,29:II
1 976723 1_976723_G_A G A 39 . AF=0.75;AQ=39 GT:DP:AD:GQ:PL:RNC 0/1:29:16,10:22:21,0,40:.. 0/1:26:12,14:24:27,0,26:.. 1/1:23:0,21:29:30,46,0:.. 1/1:31:0,31:38:39,57,0:.. 1/1:29:0,29:37:38,58,0:.. 0/1:34:14,19:28:29,0,32:.. 1/1:45:0,43:28:29,46,0:.. 0/1:11:5,6:27:27,0,41:.. 1/1:37:1,33:27:28,31,0:.. 0/1:29:21,8:16:16,0,26:..
1 976745 1_976745_CG_C CG C 17 . AF=0.5;AQ=17 GT:DP:AD:GQ:PL:RNC ./.:13:.:.:0,0,0:OO ./1:20:.,8:.:0,0,0:O. 1/1:19:3,15:10:13,15,0:.. 1/1:23:2,20:12:15,22,0:.. 1/1:20:0,18:14:17,35,0:.. ./.:10:.:.:0,0,0:OO 1/1:31:4,24:2:5,13,0:.. ./1:8:.,4:.:0,0,0:O. ./.:21:15,4:7:0,5,21:II ./.:17:14,3:4:0,1,14:II
1 976747 1_976747_C_A C A 23 . AF=0.45;AQ=23 GT:DP:AD:GQ:PL:RNC ./.:9:3,6:10:0,9,20:II ./.:10:.:.:0,0,0:OO 1/1:17:2,15:14:17,30,0:.. 1/1:22:2,20:14:17,32,0:.. 1/1:18:2,16:20:23,39,0:.. ./.:10:.:.:0,0,0:OO 1/1:25:1,24:6:9,28,0:.. ./.:3:.:.:0,0,0:OO 0/1:19:15,4:10:9,0,31:.. ./.:4:1,3:12:0,13,16:II
I cant really see any obvious difference between these lines. can you help me if this error is already in the .vcf file and OpenCRAVAT is supposed to skip these cases or just a bug ?
Thank you in advance !
The text was updated successfully, but these errors were encountered:
hi all,
I am trying to annotate a project .vcf file retrieved from GLnexus with OpenCRAVAT.
the .bcf file file gets converted to an .vcf file with:
bcftools view <bcf_file> | bgzip -c > pvcf_all_glnexus.vcf.gz
oc is installed with
conda install open-cravat==2.2.1
.if I run this file with
oc run -l hg38 -t csv -x pvcf_all_glnexus.vcf.gz
for most of the lines it works perfectly but for some I get the following errors in the err log for multiple lines:
the subset of the input .vcf file looks like this (2. and 5. line are problematic, one line before and after the error is included for comparison) :
I cant really see any obvious difference between these lines. can you help me if this error is already in the .vcf file and OpenCRAVAT is supposed to skip these cases or just a bug ?
Thank you in advance !
The text was updated successfully, but these errors were encountered: