Homozygot genotype information but SNP is heterozygous

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4.9 years ago

mw ▴ 10

I called variants by freebayes and samtools and I got variants which had a 1/1 genotyping information but they should had a 0/1 genotyping information based on the information in the vcf file. Have someone a solution for this?

Example:

Chr02 401564 . G C 753.078 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=59;CIGAR=1X;DP=317;DPB=317;DPRA=0;EPP=3.34154;EPPR=6.0605;GTI=0;LEN=1;MEANALT=2;MQM=33.5763;MQMR=3.29572;NS=1;NUMALT=1;ODDS=140.865;PAIRED=0.915254;PAIREDR=0.793774;PAO=0;PQA=0;PQR=0;PRO=0;QA=2140;QR=9653;RO=257;RPL=27;RPP=3.93042;RPPR=3.22153;RPR=32;RUN=1;SAF=55;SAP=98.7391;SAR=4;SRF=100;SRP=30.4621;SRR=157;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:317:257,59:257:9653:59:2140:-82.5116,-21.8863,0

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ADD COMMENT • link 4.9 years ago by mw ▴ 10

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Here looking at DP, DPA and DPB you have 317 reads out ouf 317 with allele B thus homozygote. Did you check the bam file in IGV ?

ADD REPLY • link 4.9 years ago by Nicolas Rosewick 11k

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RO and AO suggest there's a 257/59 split on things, so it's probably falling under either the call off point for a heterozygote or the AO reads are low quality.

ADD REPLY • link 4.9 years ago by User 59 13k

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but they should had a 0/1 genotyping information based on the information in the vcf file

What makes you conclude that?

ADD REPLY • link 4.9 years ago by WouterDeCoster 47k

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