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tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV
MIT License
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all genotype is missing ./. #156

Open lgbTime opened 1 week ago

lgbTime commented 1 week ago

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 commented 1 week ago

Hello, @lgbTime

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

Best, Shuqi

lgbTime commented 1 week ago

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

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