Hi.
I have one question when I study about DELLY paper.
(DELLY: structural variant discovery by integrated paired-end and split-read analysis.)
In paper, DELLY(tool of detecting Structural variation) records non-mapped read one alignment direction, which can be inferred from the mapped read and the default library orientation.
I wonder the default library orientation. Is it the default value in DELLY tool or commonly used for detecting SV?
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written
by
lee.jingu0626 •
1 answer
DELLY computes the default read-pair orientation and the paired insert size using the input BAM file. In paired-end libraries, the two mates can come from the opposite strand (Illumina) or the same strand (SOLiD). DELLY will determine the read-pair orientation and paired insert size for you and you dont have to worry about providing these information. It will then identify discordantly mapped read-pairs that either have an anomalous orientation or an insert size greater than the expected range to detect SVs.
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written
by
Ashutosh Pandey
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