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2 hours ago by

Hello,
I am trying DELLY v0.8.2 for the first time, using ~x40 coverage data on a plant genome. The bam file was obtained by running bwa mem, then sorting and indexing the result.
I am using default params for DELLY. My run results in a bcf file with no data (i.e. header is present, but no variants detected) and prints the following message to stdout:

Sample:SRR1945819_map_to_pan.sort,ReadSize=51,Median=407,MAD=11,UniqueDiscordantPairs=230596

I find it very unlikely that there are no SVs between my sample and the reference, so I guess something is wrong with my data or the way I use DELLY.
Any ideas on what might be going wrong?
Thanks!

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liorglic150



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