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Hi!
I was trying to compare the snp calling from GATK and Samtools. But GATK does not report the FQ (phred-scaled probability of there being two or more different alleles), is there a way of calculating it from the data GATK gives?
GATK:
chr1 754182 rs3131969 A G 172.34 . AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.1343;MQ=47.97;MQ0=0;QD=4.66;SB=27.08
;sumGLbyD=5.47 GT:AD : DP:GQ:PL 0/1:27,9:34:99:202,0,920
mpileup:
chr1 754182 . A G 62 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=16,8,8,0;MQ=47;FQ=65;PV4=0.081,0.11,4.7e-05,1 GT:PL:GQ 0/1:92,0,
255:95
Thanks!
I was trying to compare the snp calling from GATK and Samtools. But GATK does not report the FQ (phred-scaled probability of there being two or more different alleles), is there a way of calculating it from the data GATK gives?
GATK:
chr1 754182 rs3131969 A G 172.34 . AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.1343;MQ=47.97;MQ0=0;QD=4.66;SB=27.08
;sumGLbyD=5.47 GT:AD : DP:GQ:PL 0/1:27,9:34:99:202,0,920
mpileup:
chr1 754182 . A G 62 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=16,8,8,0;MQ=47;FQ=65;PV4=0.081,0.11,4.7e-05,1 GT:PL:GQ 0/1:92,0,
255:95
Thanks!
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