Info Error: max_aaf_all not found in INFO

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Andrew O

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Sep 20, 2019, 3:00:15 PM9/20/19
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Hi,

I'm testing vcfanno using the conf file here, as recommended in the vcf2db documentation. When I run it with this a VCF just containing this variant I get an error:

...

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|CCDS|SIFT|PolyPhen|HGVS_OFFSET|APPRIS|Aloft_Confidence|Aloft_Fraction_transcripts_affected|Aloft_pred|Aloft_prob_Dominant|Aloft_prob_Recessive|Aloft_prob_Tolerant|Ancestral_allele|CADD_phred|CADD_raw|DEOGEN2_pred|DEOGEN2_score|FATHMM_pred|FATHMM_score|GenoCanyon_score|Interpro_domain|LRT_pred|LRT_score|M-CAP_pred|M-CAP_score|MPC_score|MVP_score|MetaLR_pred|MetaLR_score|MetaSVM_pred|MetaSVM_score|MutPred_AAchange|MutPred_Top5features|MutPred_protID|MutPred_score|MutationAssessor_pred|MutationAssessor_score|MutationTaster_pred|MutationTaster_score|PROVEAN_pred|PROVEAN_score|PrimateAI_pred|PrimateAI_score|REVEL_rankscore|REVEL_score|Reliability_index|VEST4_score|clinvar_clnsig|clinvar_review|clinvar_trait|LoF|LoF_filter|LoF_flags|LoF_info|MES-NCSS_downstream_acceptor|MES-NCSS_downstream_acceptor_seq|MES-NCSS_downstream_donor|MES-NCSS_downstream_donor_seq|MES-NCSS_upstream_acceptor|MES-NCSS_upstream_acceptor_seq|MES-NCSS_upstream_donor|MES-NCSS_upstream_donor_seq|MES-SWA_acceptor_alt|MES-SWA_acceptor_alt_context|MES-SWA_acceptor_alt_frame|MES-SWA_acceptor_alt_seq|MES-SWA_acceptor_diff|MES-SWA_acceptor_ref|MES-SWA_acceptor_ref_comp|MES-SWA_acceptor_ref_comp_seq|MES-SWA_acceptor_ref_context|MES-SWA_acceptor_ref_frame|MES-SWA_acceptor_ref_seq|MES-SWA_donor_alt|MES-SWA_donor_alt_context|MES-SWA_donor_alt_frame|MES-SWA_donor_alt_seq|MES-SWA_donor_diff|MES-SWA_donor_ref|MES-SWA_donor_ref_comp|MES-SWA_donor_ref_comp_seq|MES-SWA_donor_ref_context|MES-SWA_donor_ref_frame|MES-SWA_donor_ref_seq|MaxEntScan_alt|MaxEntScan_alt_seq|MaxEntScan_diff|MaxEntScan_ref|MaxEntScan_ref_seq|ada_score|rf_score">

...

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1005NIH

21 45705988 rs3746964 T C 5818.83 PASS AC=7;AF=0.019;AN=264;BaseQRankSum=-2.647;ClippingRankSum=0.377;DB;DP=5481;ExcessHet=3.0519;FS=0;InbreedingCoeff=-0.0192;MLEAC=7;MLEAF=0.027;MQ=60;MQRankSum=0.104;POSITIVE_TRAIN_SITE;QD=16.3;ReadPosRankSum=1.2;SOR=0.693;VQSLOD=17.89;culprit=FS;hetAltAB=0.491;CSQ=C|synonymous_variant|LOW|AIRE|ENSG00000160224|Transcript|ENST00000291582|protein_coding|1/14||ENST00000291582.5:c.99T>C|ENSP00000291582.5:p.Ala33%3D|226/2257|99/1638|33/545|A|gcT/gcC|||1||HGNC|360|YES|CCDS13706.1|||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.066|CAGGTGGGC|||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000329347|protein_coding|||||||||||4702|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000337909|retained_intron|||||||||||4650|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000355347|protein_coding|||||||||||4702|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000397994|retained_intron|||||||||||4650|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|non_coding_transcript_exon_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000527919|retained_intron|1/14||ENST00000527919.1:n.260T>C||260/2409|||||||1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.066|CAGGTGGGC|||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|non_coding_transcript_exon_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000530812|retained_intron|1/12||ENST00000530812.1:n.268T>C||268/4306|||||||1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.066|CAGGTGGGC|||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC||||||| GT:AD:DP:GQ:PL 0/1:36,41:77:99:1000,0,980

[truncating the header to save space]


vcfanno -base-path /gemini_data/ -lua custom.lua gem.conf $vcf > $out


=============================================

vcfanno version 0.3.2 [built with go1.12.1]


see: https://github.com/brentp/vcfanno

=============================================

vcfanno.go:115: found 50 sources from 17 files

vcfanno.go:156: falling back to non-bgzip

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_Adj' from '/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_AFR' from '/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_AMR' from '/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_EAS' from '/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_FIN' from '/gemini/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_NFE' from '/gemini/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_OTH' from '/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_SAS' from '/gemini_data//ExAC.r0.3.sites.vep.tidy.vcf.gz' can result in out-of-order values when the query is multi-allelic

api.go:812:        : this is not an issue if the query has been decomposed.

vcfanno.go:194: Info Error: max_aaf_all not found in INFO >> this error/warning may occur many times. reporting once here...

vcfanno.go:248: annotated 1 variants in 0.08 seconds (13.2 / second)



vcfanno quits and the output vcf does indeed get annotated and max_aaf_all is added:

21 45705988 rs3746964 T C 5818.8 PASS AC=7;AF=0.019;AN=264;BaseQRankSum=-2.647;ClippingRankSum=0.377;DB;DP=5481;ExcessHet=3.0519;FS=0;InbreedingCoeff=-0.0192;MLEAC=7;MLEAF=0.027;MQ=60;MQRankSum=0.104;POSITIVE_TRAIN_SITE;QD=16.3;ReadPosRankSum=1.2;SOR=0.693;VQSLOD=17.89;culprit=FS;hetAltAB=0.491;CSQ=C|synonymous_variant|LOW|AIRE|ENSG00000160224|Transcript|ENST00000291582|protein_coding|1/14||ENST00000291582.5:c.99T>C|ENSP00000291582.5:p.Ala33%3D|226/2257|99/1638|33/545|A|gcT/gcC|||1||HGNC|360|YES|CCDS13706.1|||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.066|CAGGTGGGC|||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000329347|protein_coding|||||||||||4702|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000337909|retained_intron|||||||||||4650|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000355347|protein_coding|||||||||||4702|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000397994|retained_intron|||||||||||4650|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|non_coding_transcript_exon_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000527919|retained_intron|1/14||ENST00000527919.1:n.260T>C||260/2409|||||||1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.066|CAGGTGGGC|||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||,C|non_coding_transcript_exon_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000530812|retained_intron|1/12||ENST00000530812.1:n.268T>C||268/4306|||||||1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.066|CAGGTGGGC|||||-2.623|TCCCACTGCTGCACGCGCTGGCCGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCCGACC|-0.324|-2.948|-2.948|ACTGCTGCACGCGCTGGCTGACC|TCCCACTGCTGCACGCGCTGGCTGACCACGACGTGGTCCCCGAGG|5|ACTGCTGCACGCGCTGGCTGACC|-10.525|GCGCTGGCCGACCACGA|1|GCGCTGGCC|0.887|-7.768|-9.638|GCGCTGGCT|GCGCTGGCTGACCACGA|5|TGGCTGACC|||||||;in_exac;ac_exac_all=1555;an_exac_all=13428;ac_exac_afr=618;an_exac_afr=1138;ac_exac_amr=19;an_exac_amr=164;ac_exac_eas=69;an_exac_eas=274;ac_exac_fin=0;an_exac_fin=10;ac_exac_nfe=211;an_exac_nfe=4128;ac_exac_oth=13;an_exac_oth=134;ac_exac_sas=625;an_exac_sas=7580;in_esp;aaf_esp_ea=0.016787537;aaf_esp_aa=0.375132837;aaf_esp_all=0.137109723;EXOME_CHIP;rs_ids=rs3746964;in_1kg;aaf_1kg_amr_float=0.1153;aaf_1kg_eas_float=0.2788;aaf_1kg_sas_float=0.0675;aaf_1kg_afr_float=0.5651;aaf_1kg_eur_float=0.0249;aaf_1kg_all_float=0.2394;clinvar_pathogenic=Benign;fitcons=0.5977;encode_consensus_gm12878=R;encode_consensus_h1hesc=unknown;encode_consensus_helas3=unknown;encode_consensus_hepg2=R;encode_consensus_huvec=unknown;encode_consensus_k562=R;gerp_elements=0;cpg_island;dgv=CopyNumber;hapmap1=9.1496;hapmap2=58.7016;af_exac_all=0.1158;af_exac_afr=0.5431;af_exac_amr=0.1159;af_exac_eas=0.2518;af_exac_nfe=0.0511;af_exac_oth=0.097;af_exac_sas=0.0825;max_aaf_all=0.5431 GT:AD:DP:GQ:PL 0/1:36,41:77:99:1000,0,980



But the lack of information in the error made me need to stop and troubleshoot.  I found that this block below was causing the error, since it's invoking the max_aaf_all field before it's been created -- it's created further on in the conf file.  Is there a rule that you can't use a field in a postannotation step that hasn't been created further up in the file?  If so, this example file in the link doesn't conform to that.

[[postannotation]]
fields=["clinvar_sig", "max_aaf_all"]
op="lua:check_clinvar_aaf(clinvar_sig, max_aaf_all, 0.005)"
name="common_pathogenic"
type="Flag"

I moved this block to the end of the conf file and re-ran.  Now I get a different error:
vcfanno.go:194: Info Error: clinvar_sig not found in INFO >> this error/warning may occur many times. reporting once here...

In this case, since I know what the variant is, it's probably because this variant is not in clinvar so it's fine and I can safely ignore it.  But is there an easy way when I see an error like this to know whether it's a problem with my conf file or whether the variant is just not in clinvar?  The error doesn't report what the variant is that caused the error so it's a bit of work to track it down and I don't want to have to troubleshoot every time I annotate a VCF.

When I add this variant (so now the VCF has two variants):

21 45706081 . G C


Here is the annotate VCF record

oleraj@ai-submit1 test_vcfanno]$ tail -n 1 2.anno.vcf 

21 45706081 . G C 99.6 PASS AC=2;AF=0;AN=264;BaseQRankSum=-0.72;ClippingRankSum=0;DP=5836;ExcessHet=3.0103;FS=5.077;InbreedingCoeff=-0;MLEAC=2;MLEAF=0.007576;MQ=60;MQRankSum=1.38;QD=3.56;ReadPosRankSum=0.72;SOR=0.105;VQSLOD=12.28;culprit=QD;hetAltAB=0.2857;CSQ=C|intron_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000291582|protein_coding||1/13|ENST00000291582.5:c.132+60G>C|||||||||1||HGNC|360|YES|CCDS13706.1|||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.230|AAGGTGGGT|||8.066|CAGGTGGGC|-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000329347|protein_coding|||||||||||4609|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000337909|retained_intron|||||||||||4557|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000355347|protein_coding|||||||||||4609|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||,C|upstream_gene_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000397994|retained_intron|||||||||||4557|1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000527919|retained_intron||1/13|ENST00000527919.1:n.293+60G>C|||||||||1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.230|AAGGTGGGT|||8.066|CAGGTGGGC|-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|AIRE|ENSG00000160224|Transcript|ENST00000530812|retained_intron||1/11|ENST00000530812.1:n.301+60G>C|||||||||1||HGNC|360|||||||||||||||||||||||||||||||||||||||||||||||||||||||6.616|CTCATGCCACCCCACTGCAGGAG|8.230|AAGGTGGGT|||8.066|CAGGTGGGC|-3.480|TGTGAGCCAGGGATAGTCCCCGCGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGCGGAAGTTCCAGGAG|-1.994|-5.475|-5.475|AGTCCCCGGGGAAGTTCCAGGAG|TGTGAGCCAGGGATAGTCCCCGGGGAAGTTCCAGGAGGACCCCGC|15|AGTCCCCGGGGAAGTTCCAGGAG|2.283|AGTCCCCGCGGAAGTTC|7|CGCGGAAGT|0.819|3.102|3.102|CGGGGAAGT|AGTCCCCGGGGAAGTTC|7|CGGGGAAGT|||||||;rs_ids=rs578064722;in_1kg;aaf_1kg_amr_float=0.0029;aaf_1kg_eas_float=0;aaf_1kg_sas_float=0;aaf_1kg_afr_float=0.0008;aaf_1kg_eur_float=0.0139;aaf_1kg_all_float=0.0033946;fitcons=0.0955;encode_consensus_gm12878=R;encode_consensus_h1hesc=R;encode_consensus_helas3=unknown;encode_consensus_hepg2=R;encode_consensus_huvec=unknown;encode_consensus_k562=R;dgv=CopyNumber;hapmap1=9.1496;hapmap2=58.7016;stam_mean=16.359;stam_names=HESC GT:AD:DP:GQ:PL 0/0:66,0:66:99:0,120,1800


and I get this warning from vcfanno:
vcfanno.go:194: Info Error: clinvar_sig not found in INFO >> this error/warning may occur many times. reporting once here...
vcfanno.go:194: Info Error: max_aaf_all not found in INFO >> this error/warning may occur many times. reporting once here...


The second variant is absent from ExAC so it doesn't get the exac annotations.  The odd thing about this warning though is that it complains about max_aaf_all instead of ac_exac_all, which is in a postannotation step further up in the file:

[[postannotation]]

fields=["ac_exac_all", "an_exac_all"]

name="af_exac_all"

op="div2"

type="Float"


I suppose the reason is that the postannotation step causing the warning has a "lua:" operation, unlike this postannotation step above -- is that correct?
op="lua:check_clinvar_aaf(clinvar_sig, max_aaf_all, 0.005)"


Is there any way to avoid these warnings by modifying the conf file or lua file with some default for the values or something?


Thanks,

Andrew






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