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Why the genotype is "./."

See original GitHub issue

Hi, Fritz,

chr1 1074252 65 N <DEL> . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=1099389;STD_quant_start=0.632456;STD_quant_stop=0.632456;Kurtosis_quant_start=-0.500000;Kurtosis_quant_stop=-0.500000;SVTYPE=DEL;RNAMES=1723761;SUPTYPE=SR;SVLEN=-25137;STRANDS=+-;STRANDS2=3,2,3,2;RE=5 GT:DR:DV ./.:.:5

why the genotype is “./.:.” ?

my command is: sniffles -m sample.sort.bam -v sample.vcf -s 5 -t 10 -l 30 -n 1 --report_BND --report_seq --report_read_strands --ignore_sd --tmp_file tmpfile --cluster --cluster_support 1 --genotype I used the version 1.0.11.

Issue Analytics

State:
Created 5 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

biomichalcommented, Mar 20, 2019

I got it. Maybe I shoud leave the computer for a while, until it is done.

Thanks

0reactions

fritzsedlazeckcommented, Mar 20, 2019

Yes. Sniffles writes out the found svs in a vcf files. Once this is all done it goes back and insert the gt value. So all is fine. I hope that helps. Fritz