Open hygine opened 4 years ago
@fritzsedlazeck V1.0.7 vcftobed have some problem like this:
v1.0.7-vcftobed 【wrong result】 Y 56883626 56883626 Y 56883666 56883666 27472 , + - INS Y 56883627 Y 56883667 MT -1 -1 MT 16568 16568 27473 , - + DUP MT 0 MT 16569 MT 2950 2950 MT 3364 3364 27474 , - - INV MT 2951 MT 3365 MT 11923 11923 MT 12275 12275 27475 , - - INV MT 11924 MT 12276 1 878420 878420 3 198124403 198124403 27476 , - + TRA 1 878421 3 198124404 1 883242 883242 20 29351520 29351520 27477 , + + TRA 1 883243 20 29351521
v1.0.5-vcftobed 【right result】 Y 56883628 56883628 Y 56883667 56883667 27472 , + - INS MT 1 1 MT 16569 16569 27473 , - + DUP MT 2952 2952 MT 3365 3365 27474 , - - INV MT 11925 11925 MT 12276 12276 27475 , - - INV 1 878422 878422 3 198124404 198124404 27476 , - + TRA 1 883244 883244 20 29351521 29351521 27477 , + + TRA
xx.vcf 【raw vcf】 Y 56883628 27472 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=Y;END=56883667;STD_quant_start=4.722288;STD_quant_stop=7.449832;Kurtosis_quant_start=0.571770;Kurto sis_quant_stop=-1.305242;SVTYPE=INS;SUPTYPE=AL;SVLEN=47;STRANDS=+-;SEQ=ACAGGGATGGAAGGCAGACACGCAAAAATCACAATCATA;RE=12;REF_strand=2,8;AF=0.545455 GT:DR:DV 0/1:10:12 MT 1 27473 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=MT;END=16569;STD_quant_start=0.474821;STD_quant_stop=0.482418;Kurtosis_quant_start=73.643881;Kurtosis_quant _stop=66.055913;SVTYPE=DUP;SUPTYPE=SR;SVLEN=16568;STRANDS=-+;RE=551;REF_strand=0,0;AF=1 GT:DR:DV 1/1:0:551 MT 2952 27474 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=MT;END=3365;STD_quant_start=207.164669;STD_quant_stop=400.061745;Kurtosis_quant_start=-0.088173;Kurtosis_quant_stop=1.050173;SVTYPE=INVDUP;SUPTYPE=SR;SVLEN=413;STRANDS=--;RE=12;REF_strand=188,200;AF=0.03 GT:DR:DV 0/0:388:12 MT 11925 27475 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=MT;END=12276;STD_quant_start=237.369964;STD_quant_stop=290.302601;Kurtosis_quant_start=-1.549944;Kurtosis_quant_stop=-0.996418;SVTYPE=INVDUP;SUPTYPE=SR;SVLEN=351;STRANDS=--;RE=17;REF_strand=17,20;AF=0.314815 GT:DR:DV 0/1:37:17 1 878422 27476 N ]3:198124404]N . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;STD_quant_start=1.378405;STD_quant_stop=1.000000;Kurtosis_quant_start=3.279799;Kurtosis_quant_stop=-0.248529;SVTYPE=BND;SUPTYPE=SR;SVLEN=0;STRANDS=-+;RE=21;REF_strand=0,0;AF=1 GT:DR:DV 1/1:0:21 1 883244 27477 N N[20:29351521[ . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;STD_quant_start=9.869144;STD_quant_stop=4.483302;Kurtosis_quant_start=-0.139085;Kurtosis_quant_stop=2.029617;SVTYPE=BND;SUPTYPE=SR;SVLEN=0;STRANDS=++;RE=13;REF_strand=3,0;AF=0.8125 GT:DR:DV 1/1:3:13
@fritzsedlazeck
hygine
commented
4 years ago hygine
commented
4 years ago
@fritzsedlazeck V1.0.7 vcftobed have some problem like this:
v1.0.7-vcftobed 【wrong result】 Y 56883626 56883626 Y 56883666 56883666 27472 , + - INS Y 56883627 Y 56883667 MT -1 -1 MT 16568 16568 27473 , - + DUP MT 0 MT 16569 MT 2950 2950 MT 3364 3364 27474 , - - INV MT 2951 MT 3365 MT 11923 11923 MT 12275 12275 27475 , - - INV MT 11924 MT 12276 1 878420 878420 3 198124403 198124403 27476 , - + TRA 1 878421 3 198124404 1 883242 883242 20 29351520 29351520 27477 , + + TRA 1 883243 20 29351521
v1.0.5-vcftobed 【right result】 Y 56883628 56883628 Y 56883667 56883667 27472 , + - INS MT 1 1 MT 16569 16569 27473 , - + DUP MT 2952 2952 MT 3365 3365 27474 , - - INV MT 11925 11925 MT 12276 12276 27475 , - - INV 1 878422 878422 3 198124404 198124404 27476 , - + TRA 1 883244 883244 20 29351521 29351521 27477 , + + TRA
xx.vcf 【raw vcf】 Y 56883628 27472 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=Y;END=56883667;STD_quant_start=4.722288;STD_quant_stop=7.449832;Kurtosis_quant_start=0.571770;Kurto sis_quant_stop=-1.305242;SVTYPE=INS;SUPTYPE=AL;SVLEN=47;STRANDS=+-;SEQ=ACAGGGATGGAAGGCAGACACGCAAAAATCACAATCATA;RE=12;REF_strand=2,8;AF=0.545455 GT:DR:DV 0/1:10:12 MT 1 27473 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=MT;END=16569;STD_quant_start=0.474821;STD_quant_stop=0.482418;Kurtosis_quant_start=73.643881;Kurtosis_quant
_stop=66.055913;SVTYPE=DUP;SUPTYPE=SR;SVLEN=16568;STRANDS=-+;RE=551;REF_strand=0,0;AF=1 GT:DR:DV 1/1:0:551
MT 2952 27474 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=MT;END=3365;STD_quant_start=207.164669;STD_quant_stop=400.061745;Kurtosis_quant_start=-0.088173;Kurtosis_quant_stop=1.050173;SVTYPE=INVDUP;SUPTYPE=SR;SVLEN=413;STRANDS=--;RE=12;REF_strand=188,200;AF=0.03 GT:DR:DV 0/0:388:12
MT 11925 27475 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=MT;END=12276;STD_quant_start=237.369964;STD_quant_stop=290.302601;Kurtosis_quant_start=-1.549944;Kurtosis_quant_stop=-0.996418;SVTYPE=INVDUP;SUPTYPE=SR;SVLEN=351;STRANDS=--;RE=17;REF_strand=17,20;AF=0.314815 GT:DR:DV 0/1:37:17
1 878422 27476 N ]3:198124404]N . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;STD_quant_start=1.378405;STD_quant_stop=1.000000;Kurtosis_quant_start=3.279799;Kurtosis_quant_stop=-0.248529;SVTYPE=BND;SUPTYPE=SR;SVLEN=0;STRANDS=-+;RE=21;REF_strand=0,0;AF=1 GT:DR:DV 1/1:0:21
1 883244 27477 N N[20:29351521[ . PASS PRECISE;SVMETHOD=Snifflesv1.0.10;STD_quant_start=9.869144;STD_quant_stop=4.483302;Kurtosis_quant_start=-0.139085;Kurtosis_quant_stop=2.029617;SVTYPE=BND;SUPTYPE=SR;SVLEN=0;STRANDS=++;RE=13;REF_strand=3,0;AF=0.8125 GT:DR:DV 1/1:3:13