Delly call - Paramaters detailed version

[Delalab]

Hi,

Can you please be more precise about these parameters: I can't seem to find the information anywhere( github, publication, google..)

1)-

  -n [ --maxreadsep ] arg (=40)      max. read separation

 Does it mean reads that are separated by more than 40 bp are discaded? Anything to do with paired-end insert?

2)-

  -m [ --minrefsep ] arg (=25)       min. reference separation

There should be at least 25 reads difference between two samples?

3)-

  -u [ --geno-qual ] arg (=5)        min. mapping quality for genotyping

&

  -q [ --map-qual ] arg (=1)         min. paired-end (PE) mapping quality

Are'nt these two redondant for PE?

4)-

  -r [ --qual-tra ] arg (=20)        min. PE quality for translocation

Another maping quality?

5)-

  -s [ --mad-cutoff ] arg (=9)       insert size cutoff, median+s*MAD

So the bigger, the wider the insert: right?

6)-

  -z [ --min-clique-size ] arg (=2)  min. PE/SR clique size

?

--

Thanks in advance !

[Andrea stacchetti]

Hi all!

I am very interested in the following question! 

I can only contribute telling you that I find only the explanation of -m written by Tobias:

Delly clusters abnormal paired-ends and every single cluster gives rise to an IMPRECISE SV call. For every IMPRECISE SV call Delly then tries to identify split-reads and one parameter that influences this split-read search is -m. In short, Delly computes a consensus sequence out of all split-read candidates and then aligns this consensus sequence to the reference requiring at least -m XXX many aligned bases to the left and right. When I wrote Delly's split-read module the average read length was 36bp-50bp so I fully agree it's a bit outdated by now and the plan is to indeed soon replace this by building a consensus from soft-clipped reads only, which seem to be fairly abundant when you have >=100bp reads. Nevertheless, Delly will always report only a subset of all paired-end calls at breakpoint resolution (PRECISE) because SVs tend to occur in repetitive regions.
I found here: https://groups.google.com/g/delly-users/c/VXbXX-6Yz_I/m/ft_SipC6eGAJ

Unluckily, I have no clue for the others

Best,

Andrea