phred score from vcf quality

Question

[bioguy24]

Is there a tool or script that calculate just a one or two digit phred score using the quality in a vcf? Thanks :).

  #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
  NA12878_BC2 chr1    949608  .       G       A       712.267 PASS  AF=0.4625;AO=260;DP=572;FAO=185;FDP=400;FR=.;FRO=215;FSAF=107;FSAR=78;F SRF =107;FSRR=108;FWDB=0.0625823;FXX=0;HRUN=1;LEN=1;MLLD=147.924;OALT=A;OID=.; OMAPALT=A;OPOS=949608;OREF=G;PB=0.5;PBP=1;QD=7.12267;RBI=0.0625867;REFB=-0.0025082;REVB=0.000737111;RO=311;SAF=141;SAR=119;SRF=154;SRR=157;SSEN=0;SSEP=0;SSSB=0.0466704;STB=0.543855;STBP=0.089;TYPE=snp;VARB=0.00322495;ANN=IRSG15  GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR0/1:712:572:400:311:215:260:185:0.4625:119:141:154:157:78:10,107:108

Answer 1

[Matt Shirley]

The QUAL field is already Phred scaled according to the spec. If you mean you want to encode this field as 2 ASCII characters you could use the +33 encoding as in FASTQ files, but take the product of the two values to achieve a larger range of integers.

[harold.smith.tarheel]

Correction of Matt's statement: It depends on your variant caller. While FreeBayes, GATK, and SAMtools/BCFtools produce PHRED quality scores, VarScan produces p-values by default (PHRED can be generated with the '--vcf-output' flag).