Illumina / strelka

Strelka2 germline and somatic small variant caller
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Allele frequency for SNV strelka2 #174

Open ruhollah2 opened 4 years ago

ruhollah2 commented 4 years ago

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

Thank you!