How to interpret genotype 0/0 in delly results

[su wang]

Hi,

I am new to structure variation analysis. I used delly2 to call structure variation, I found a lot of variations with a genotype 0/0. What does 0/0 mean? Does it mean wild type? If it is, why the variants called here.

Some examples here:

1 1113132 DEL00000021 G <DEL> . PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.7.6;CHR2=1;END=1113387;PE=2;MAPQ=37;CT=3to5;CIPOS=-4,4;CIEND=-4,4;INSLEN=0;HOMLEN=3;SR=7;SRQ=0.992481;CONSENSUS=CAGCAGGAATCCTGGGTGCTGAGGTCCCATGAGAAGGTGCAGACGGCTGCCTCAGTTTCCCCACCTTCCCCTGCCCGTGGGCTTCCTCGTTGTCTCCTTCCCTCCTGTCACTCAGGCGGGGCAGGGAGGGGCA;CE=1.92195 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-15.5227,-159.369:157:PASS:9454:20195:9969:2:66:3:52:0

1 1317697 DEL00000034 CACCCTTCCCAACAATCCACTAACAATCCAGAGGCCACCACCCCTTCCCAACAATCCACTAACAATCCAGAGGTCA C . PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.7.6;CHR2=1;END=1317773;PE=0;MAPQ=23;CT=3to5;CIPOS=-4,4;CIEND=-4,4;INSLEN=0;HOMLEN=4;SR=10;SRQ=0.983193;CONSENSUS=TCCAGTAACAATCCAGAGGTCCCCCCCCCTTCCCAACAATCCAGTAACAATCCAGAGGTCACCACCCTTCCCAACAATCCAGTAACAATCCAGAGGCCACCACCCCTTCCCAACAAT;CE=1.80181 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-35.06,-449.373:10000:PASS:4790:14295:8077:2:0:0:174:10

1 1519716 DUP00000006 C <DUP> . PASS PRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv0.7.6;CHR2=1;END=1524973;PE=16;MAPQ=37;CT=5to3;CIPOS=-36,36;CIEND=-36,36;INSLEN=0;HOMLEN=48;SR=5;SRQ=1;CONSENSUS=GCTCACTGCAAGCTCCCCCTCCCAGGTTCACCCCATTCTCCTGCCTCAGCCTCCCGAGTAACTGGGACTACAGGCACCCACCACCACACCCGGCTAATTTT;CE=1.86603 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-2.10875,-33.6103:21:PASS:2057:5209:1932:3:62:16:11:1

1 2583654 DUP00000021 A <DUP> . PASS PRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv0.7.6;CHR2=1;END=2615723;PE=24;MAPQ=37;CT=5to3;CIPOS=-17,17;CIEND=-17,17;INSLEN=0;HOMLEN=16;SR=10;SRQ=0.956897;CONSENSUS=CCGGCAGCCTGGAGCGGCCCCCACGCCCACAGGCAAGCATCTGACAGCCTGGAGCAGCACCCACACCCCCAGGTGAGCATCCGACAGCCTGGAACAGCACCCACACGCCCAGGTGA;CE=1.79499 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-112.174,-1000:10000:PASS:12053:47191:55622:1:455:122:376:0

1 11262144 INV00000013 G <INV> . PASS PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.7.6;CHR2=1;END=16949224;PE=2;MAPQ=37;CT=5to5;CIPOS=-19,19;CIEND=-19,19;INSLEN=0;HOMLEN=25;SR=10;SRQ=0.994318;CONSENSUS=CTAAATAGTAAATCTTAAACAGCCATTTAAAATTTGGTTTACAGGCTGGGCATTGTGGCTCCTGCCTGTAATCTCAGCACTTTGGGAGGCCGAAGTGGGCAGATCACCTGAGGTCGAGAGTTCGAGACCAGCTTGACCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAT;CE=1.98896 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-32.7509,-346.639:10000:PASS:1938014:3582583:1953810:2:58:2:109:0

Anyone can help me about this?

Thanks!

[Tobias Rausch]

Delly tries to maximize sensitivity during SV discovery. The genotyping, however, is very conservative and involves a re-alignment of reads against the reference and the alternative haplotype so it can indeed happen that an SV is discovered but then genotyping settles on 0/0 (homozygous reference). In your second example, for instance, you have 174 reads supporting the reference (RR field) but only 10 supporting ALT (RV). Assuming diploidy, the most likely genotype is 0/0 in this case. For germline SVs, you should always filter out such cases and delly filter does this. For cancer it's mostly a matter of tumor purity and heterogeneity so even SVs with very low support can sometimes be true and again, delly filter offers here some command-line options in the somatic mode to filter based on this so-called variant allele frequency.

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