Normalizing fails due to incorrect column count
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5.0 years ago
andrewl ▴ 10

I have a reasonably standard VCF file:

##source=freeBayes v0.9.15-3-g6022d6a

##reference=/vbin/ref/hg19.fa

...

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown Sample1

chr10 61372 . CAT CT 285.58 PASS AB=0;ABP=0;AC=4;ADP=10;AF=1;AN=4;AO=9;CIGAR=1M1D1M;DP=9;DPB=6;DPRA=0;EPP=3.25157;EPPR=0;GTI=0;HET=0;HOM=1;LEN=1;MEANALT=1;MQM=33.6667;MQMR=0;NC=0;NS=1;NUMALT=1;ODDS=15.9832;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=348;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=8;SAP=14.8328;SAR=1;SF=0,1;SRF=0;SRP=0;SRR=0;TYPE=del;WT=0 GT:ADR:PVAL:ADF:GL:RDF:QA:RDR:DP:SDP:RD:ABQ:QR:GQ:RO:RBQ:AD:AO:FREQ 1/1:.:.:.:-10,-2.70927,0:.:348:.:9:.:.:.:0:.:0:.:.:9

I am trying to normalize it and am getting the following error in both bcftools and vt normalize:

[vcf.c:2148 vcf_parse_format] Number of columns at chr10:61372 does not match the number of samples (1 vs 2).

Any thoughts on what might be driving this?

normalize vcf • 1.2k views
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