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

?

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Thanks in advance !