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freebayes / freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.
http://arxiv.org/abs/1207.3907
MIT License
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FORMAT/GT value does NOT match --min-alternate-fraction param? #412

Closed wangyugui closed 6 years ago

wangyugui commented 7 years ago

Hi.

FORMAT/GT value does NOT match --min-alternate-fraction param?

freebayes version: v1.1.0-22-gf439104 freebayes param:--min-alternate-count 3 --min-alternate-total 6 --min-coverage 10 --min-alternate-fraction 0.05 --use-best-n-alleles 15 --pooled-continuous

vcf file:

1       16949   .       A       C       112.09  .       
AB=0.26834;ABP=244.471;AC=2;AF=0.25;AN=8;AO=164;CIGAR=1X;DP=715;DPB=715;
DPRA=0;EPP=3.06326;EPPR=6.32465;GTI=1;LEN=1;MEANALT=1;MQM=21.5793;
MQMR=14.0436;NS=4;NUMALT=1;ODDS=21.8907;PAIRED=1;PAIREDR=0.994555;PAO=0;PQA=0;
PQR=0;PRO=0;QA=6585;QR=22172;RO=551;RPL=28;RPP=157.45;RPPR=9.00451;RPR=136;
RUN=1;SAF=107;SAP=36.112;SAR=57;SRF=321;SRP=35.6454;SRR=230;TYPE=snp;technology.illumina=1

GT:DP:AD:RO:QR:AO:QA:GL 

0/0:91:79,12:79:3133:12:457:0,-7.36787,-79.5949 
0/1:232:170,62:170:6855:62:2505:-29.9354,0,-90.5213     
0/1:286:209,77:209:8493:77:3097:-1.57856,0,-75.885      
0/0:106:93,13:93:3691:13:526:0,-12.5982,-106.915

the GT value should be 0/1 when AD(79,12) and --min-alternate-fraction 0.05 ?

wangyugui commented 7 years ago

or what is the suggest genotype likelihoods param that match --min-alternate-fraction 0.05 ?

wangyugui commented 7 years ago

'--pooled-discrete --allele-balance-priors-off --report-genotype-likelihood-max ' does not help too much.

I can use 'bcftools filter --set-GTs' or 'bcftools plugin setGT' to process vcf directly.

but is there a param of freebayes to let FORMAT/GT value match --min-alternate-fraction param?

wangyugui commented 6 years ago

The GT is set to the most close one of 0/1; 0/1; 1/1;

Allele Bias is not considered.