hi:
i use the vardict v1.8.3 to call snv indel, and use the option -3 to move indels to 3-prime if alternative alignment can be achieved, and i notice that when use the opthion -3, the pos of the indel will be change but the ref base not change. such as:
one record:
chr13 28592634 . CATG C 208 PASS SAMPLE=g800idt;TYPE=Deletion;DP=4680;VD=93;AF=0.0199;BIAS=2:2;REFBIAS=2350:2231;VARBIAS=55:38;PMEAN=43.8;PSTD=1;QUAL=31.9;QSTD=1;SBF=0.1431;ODDRATIO=1.37398496860444;MQ=60;SN=186;HIAF=0.0202;ADJAF=0.0017;SHIFT3=2;MSI=1;MSILEN=1;NM=0.4;HICNT=93;HICOV=4598;LSEQ=ACAACATAGTTGGAATCACT;RSEQ=ATATCTCGAGCCAATCCAAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:4680:93:4581,93:0.0199:2350,2231:55,38
and the igv shows：
when i use the opthion -3 ,the record is:
chr13 28592636 . CATG C 208 PASS SAMPLE=g800idt;TYPE=Deletion;DP=4680;VD=93;AF=0.0199;BIAS=2:2;REFBIAS=2350:2231;VARBIAS=55:38;PMEAN=43.8;PSTD=1;QUAL=31.9;QSTD=1;SBF=0.1431;ODDRATIO=1.37398496860444;MQ=60;SN=186;HIAF=0.0202;ADJAF=0.0017;SHIFT3=2;MSI=1;MSILEN=1;NM=0.4;HICNT=93;HICOV=4598;LSEQ=AACATAGTTGGAATCACTCA;RSEQ=ATATCTCGAGCCAATCCAAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:4680:93:4581,93:0.0199:2350,2231:55,38
and i think the record may be:
chr13 28592636 . TGAT T
hi: i use the vardict v1.8.3 to call snv indel, and use the option -3 to move indels to 3-prime if alternative alignment can be achieved, and i notice that when use the opthion -3, the pos of the indel will be change but the ref base not change. such as:
one record: chr13 28592634 . CATG C 208 PASS SAMPLE=g800idt;TYPE=Deletion;DP=4680;VD=93;AF=0.0199;BIAS=2:2;REFBIAS=2350:2231;VARBIAS=55:38;PMEAN=43.8;PSTD=1;QUAL=31.9;QSTD=1;SBF=0.1431;ODDRATIO=1.37398496860444;MQ=60;SN=186;HIAF=0.0202;ADJAF=0.0017;SHIFT3=2;MSI=1;MSILEN=1;NM=0.4;HICNT=93;HICOV=4598;LSEQ=ACAACATAGTTGGAATCACT;RSEQ=ATATCTCGAGCCAATCCAAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:4680:93:4581,93:0.0199:2350,2231:55,38
and the igv shows：
when i use the opthion -3 ,the record is: chr13 28592636 . CATG C 208 PASS SAMPLE=g800idt;TYPE=Deletion;DP=4680;VD=93;AF=0.0199;BIAS=2:2;REFBIAS=2350:2231;VARBIAS=55:38;PMEAN=43.8;PSTD=1;QUAL=31.9;QSTD=1;SBF=0.1431;ODDRATIO=1.37398496860444;MQ=60;SN=186;HIAF=0.0202;ADJAF=0.0017;SHIFT3=2;MSI=1;MSILEN=1;NM=0.4;HICNT=93;HICOV=4598;LSEQ=AACATAGTTGGAATCACTCA;RSEQ=ATATCTCGAGCCAATCCAAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:4680:93:4581,93:0.0199:2350,2231:55,38
and i think the record may be: chr13 28592636 . TGAT T
why the ref base not change?