Questions: delly genotype for SR and RV

[zhangshouwei309194]

Dear author：
When I used delly for SV detecting，i found a questions that maked me confused. For example: SR indicates the number of split reads is 39, but RV (the number of junction reads) is 0. For junction reads and split reads, it should be the same notation. Is there any reasons in genotyping？
8 121299546 BND00008260 A [10:123241058[A 2340 PASS PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv1.1.6;END=121299547;CHR2=10;POS2=123241058;PE=0;MAPQ=0;CT=5to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=60;INSLEN=0;HOMLEN=5;SR=39;SRQ=1;CONSENSUS=CTCTCCATAACCAAGAAAATAAACATGCCAAGAGGAATTTGGTGAGTAAACAATGTTAAGTCCTAAGAGCTGCTAATGGGACCACTTTGAGCCATGAACTAATAAATCTCCACCACATCAAAAGAGAACTTTTTGCTTACAATGATAAAAACGAAATTTTGTCCTAAATGGAACCGTTTTTCTTGAGCATATGGTAATGATTTTCAGAAGGAAAGAAACTTCGATTTTTATATCCACCAGAC;CE=1.92421 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-75.1615,-768.704:10000:PASS:338:4712:4374:2:0:0:250:0
Look forward to your reply!
Thank you .
Yours sincerely
Phillip！

[tobiasrausch]

Is this maybe some targeted data? Delly stops SR genotyping at 250 reads for performance reasons and if you have some deep-coverage targeted data (>>100x) then a low frequency variant will be incorrectly genotyped. You need to set -a to something much higher than your actual coverage. So to be safe: delly call -a 100000 ...

[AndreasSandJespersen]

Hi I don't mean to be rude, but I don't think issue #383 should be closed.

[tobiasrausch]

Re-opened #383.