all genotype is missing ./.

[lgbTime]

i use pip to intall cuteSV, and my command is : "cuteSV CRR302668.fastq.gz.bam Db-1_genome.fa Col-CEN_cuteSV.vcf ./".
the pogram did generate the vcf file, but i gent the results as below all the GT information is missing ./. :
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NULL
Db-Chr1 21828 cuteSV.BND.0 t [Db-Chr3:2633736[N . PASS PRECISE;SVTYPE=BND;RE=17;RNAMES=NULL GT:DR:DV:PL:GQ ./.:.:17:.,.,.:.
Db-Chr1 22992 cuteSV.INS.0 g gATTCTTCATTCATGAAATCATTATTCCAAGGGTTTTGGGATAAGA . PASS PRECISE;SVTYPE=INS;SVLEN=45;END=22992;CIPOS=-2,2;CILEN=-0,0;RE=23;RNAMES=NULL GT:DR:DV:PL:GQ ./.:.:23:.,.,.:.
Db-Chr1 23537 cuteSV.BND.1 A N]Db-Chr3:2633735] . PASS PRECISE;SVTYPE=BND;RE=20;RNAMES=NULL GT:DR:DV:PL:GQ ./.:.:20:.,.,.:.
Db-Chr1 96131 cuteSV.BND.2 T N[Db-Chr5:20967680[ . PASS PRECISE;SVTYPE=BND;RE=80;RNAMES=NULL GT:DR:DV:PL:GQ ./.:.:80:.,.,.:.

what can i do to fix the issue?

[Meltpinkg]

Hello, @lgbTime

You can add the parameter --genotype to activate the genotyping module, then it will output the GT information.

Best,
Shuqi

[lgbTime]

thank

…

---- Replied Message ---- | From | ***@***.***> | | Date | 11/11/2024 16:33 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [tjiangHIT/cuteSV] all genotype is missing ./. (Issue #156) | Hello, @lgbTime You can add the parameter --genotype to activate the genotyping module, then it will output the GT information. Best, Shuqi — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>