[W::vcf_parse_format] Extreme FORMAT/AO value encountered and set to missing at chr8:160826

[vappiah]

Dear Developers, I encountered the error message above after normalizing my bcftools and using the view command

I used this command to normalize bcftools norm -m-both -f data/ref/chr8.fa VCF/variants.vcf.gz -O v -o VCF/variants.normalized.vcf

I tried to count the number of snps and that is when I got the message. bcftools view -v snps VCF/variants.normalized.vcf |grep -v -c '^#'

Note: the bcftools view command does not generate the error message when I use it on the original vcf

Please advise.

[pd3]

This comes from the VCF parser in htslib when a value exceeds the maximum integer representable in 32 bits. It is a bit odd that this should happen for FORMAT/AO, I suspect there was a problem somewhere in converting missing value between BCF and VCF at some point.

[vappiah]

I guess I can still use the normalized vcf.

I can send you the original VCF in case you want to examine it.

[pd3]

Sure. You can just look in the original VCF and grep for position 160826 on chr8 and see what values there are for the FORMAT/AO field.

[vappiah]

Hi @pd3 Here is the output for the grep command.

chr8 160826 . C T 1139.53 . DPB=73;EPPR=5.63551;GTI=0;MQMR=60;NS=1;NUMALT=1;ODDS=80.0471;PAIREDR=1;PQR=0;PRO=0;QR=1847;RO=67;RPPR=5.63551;SRF=16;SRP=42.7126;SRR=51;DP=124;AB=0;ABP=0;AF=1;AO=44;CIGAR=3M1X;DPRA=0;EPP=12.6832;LEN=1;MEANALT=5;MQM=60;PAIRED=1;PAO=1;PQA=29;QA=1434;RPL=8;RPP=41.702;RPR=36;RUN=1;SAF=7;SAP=47.4268;SAR=37;TYPE=snp;technology.Illumina=1;AN=4;AC=2GT:DP:AD:RO:QR:AO:QA:GL 0/0:73:67,.:67:1847:.:.:0,.,. 1/1:51:1,44:1:39:44:1434:-125.592,-10.0141,0 ./.:.:.:.:.:::. chr8 160826 . C T 1783.34 . DPB=69.6667;EPPR=5.18177;GTI=0;MQMR=60;NS=1;NUMALT=1;ODDS=95.5437;PAIREDR=1;PQR=57;PRO=2;QR=2;RO=1;RPPR=5.18177;SRF=0;SRP=5.18177;SRR=1;DP=67;AB=0;ABP=0;AF=1;AO=66;CIGAR=2M1X;DPRA=0;EPP=3.53672;LEN=1;MEANALT=1;MQM=60;PAIRED=1;PAO=3;PQA=91;QA=2097;RPL=27;RPP=7.74806;RPR=39;RUN=1;SAF=10;SAP=72.629;SAR=56;TYPE=snp;technology.Illumina=1;AN=2;AC=2GT:DP:AD:RO:QR:AO:QA:GL 1/1:67:1,66:1:2:66:2097:-188.514,-20.2481,0 ./.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:. chr8 160826 . C T 3223.24 . DPB=115;EPPR=7.35324;GTI=0;MQMR=60;NS=1;NUMALT=1;ODDS=154.143;PAIREDR=1;PQR=0;PRO=0;QR=12;RO=2;RPPR=3.0103;SRF=1;SRP=3.0103;SRR=1;DP=115;AB=0;ABP=0;AF=1;AO=112;CIGAR=1X;DPRA=0;EPP=16.1167;LEN=1;MEANALT=2;MQM=59.8929;PAIRED=1;PAO=0;PQA=0;QA=3701;RPL=41;RPP=20.4596;RPR=71;RUN=1;SAF=32;SAP=47.6806;SAR=80;TYPE=snp;technology.Illumina=1;AN=2;AC=2GT:DP:AD:RO:QR:AO:QA:GL ./.:.:.:.:.:.:.:.

[pd3]

Can you also show full header please?