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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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Is RC the same as SR? #83

Closed ggrimes closed 5 years ago

ggrimes commented 5 years ago

Is the Read count (RC) the same as the number of Split Reads that support the variant?

Thanks

Graeme

keiranmraine commented 5 years ago

No,

Pairs spanning (PS) are those pairs where the insert size/orientation was disrupted and were used to form the group before refinement (aberrantly paired).

Reads contributing (RC) are those velvet indicated as being part of the assembly across the breakpoint.

##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Count of pairs that span this breakpoint">
##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Count of countributing reads">

(typo in that header line)

The split reads are only used "as is" in some of the filtering steps when trying to reduce the number of events passed to assembly.