According to strelka2 user guide, allele frequency can be computed for SNV from VCF output as:
efCounts = Value of FORMAT column $REF + “U” (e.g. if REF="A" then use the value in FOMRAT/AU)
altCounts = Value of FORMAT column $ALT + “U” (e.g. if ALT="T" then use the value in FOMRAT/TU)
tier1RefCounts = First comma-delimited value from $refCounts
tier1AltCounts = First comma-delimited value from $altCounts
Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts)
I have hard time, however, in connecting the symbols in the FORMAT field to their corresponding numerical values in the NORMAL and TUMOR fields. For example for these two locations, how do you connect the symbols DP:FDP:SDP:SUBDP:AU:CU:GU:TU to their corresponding values in the NORMAL and TUMOR field?
chr1 4345650 . C T . PASS SOMATIC;QSS=153;TQSS=1;NT=ref;QSS_NT=154;TQSS_NT=1;SGT=CC->CT;DP=164;MQ=60.00;MQ0=0;ReadPosRankSum=0.69;SNVSB=0.00;SomaticEVS=19.98 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 63:1:0:0:0,0:62,63:0,0:0,0 98:1:0:0:0,0:58,58:0,0:39,43
chr1 24021818 . C A . PASS SOMATIC;QSS=30;TQSS=1;NT=ref;QSS_NT=30;TQSS_NT=1;SGT=CC->AC;DP=145;MQ=60.00;MQ0=0;ReadPosRankSum=-0.54;SNVSB=0.00;SomaticEVS=7.12 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 68:0:0:0:0,0:68,70:0,0:0,0 75:0:0:0:2,2:72,72:0,0:1,1
According to strelka2 user guide, allele frequency can be computed for SNV from VCF output as:
I have hard time, however, in connecting the symbols in the
FORMATfield to their corresponding numerical values in theNORMALandTUMORfields. For example for these two locations, how do you connect the symbolsDP:FDP:SDP:SUBDP:AU:CU:GU:TUto their corresponding values in theNORMALandTUMORfield?Thank you!