What does Consensus mean in the output file?

[Weini Huang]

Dear all, 

Could anyone help on understanding the consensus string?  

Here is an example of a 1kb deletion at chr6:10264422-10265265 found by Delly.  I would like to know what the consensus sequence mean for this deletion? I see that Tobias mentioned to use BLAT to map it. But I couldn't understand it very well. Thank you very much for your help. 

Best,

Weini

chr6 10264422 DEL00000077 T <DEL> . PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.7.7;CHR2=chr6;END=10265265;PE=47;MAPQ=22;CT=3to5;CIPOS=-18,18;CIEND=-18,18;INSLEN=0;HOMLEN=17;SR=10;SRQ=1;CONSENSUS=TTCTCTAATAATTAGTGATGTTGAGCATTTTTTCATATGTTTTTTGGCCACTTGTATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTTGCCCACTTTTTGATAGGGTTGTTTGATTTTTTTCTTGTAAATTTGTTTAAGTTCTTTGTAGATTCTG;CE=1.75334 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-76.4508,-7.37652,0:74:PASS:112:0:95:0:2:21:0:25 1/1:-114.288,-10.1226,0:101:PASS:150:0:144:0:2:25:0:34

[Joel Martin]

It may be simplest to try

go to genome.ucsc.edu -> Tools -> Blat

paste in that sequence and submit. Click browse  on the first result at 100% ID. You'll see it's the sequence with the deletion deleted, as it were.

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