Parameters for max reads and chunk size

[yoyosef]

Hello, we are running cases on trios and we're trying to find structural variants mainly in the child. I am from a computer science background so I don't have full picture of how some of these parameters could affect the results.

The man page offered these flags as input: max_reads -x
max_chunk -c How does the tuning of these parameters affect the results?

Thanks,

Yosef

[walaj]

Hi Yosef, Thanks for your patience with this. No one (even me) ever really tunes those. Max-reads is just a stopping param in case there is some region of the BAM with millions of reads all in one spot (usually a centromere and other places where it's better to just have svaba move along). Max chunk also just changes the size of the anchor window, but svaba should not be sensitive to this parameter (I never change it). Best, Jeremiah

[wangxlab]

Hi, 'Max chunk' is the same as '--chunk-size' parameter, right? Could you explain a little more about '--chunk-size' parameter. I can't decide whether I should set 0 or 25000 (default).

-c, --chunk-size Size of a local assembly window (in bp). Set 0 for whole-BAM in one assembly. [25000]

And, when you have time, could you explain a little more about '--read-tracking' and '--error-rate' parameters? It is hard to understand the meaning of the parameters and can't decide what value I should use for the parameters. If there is an instruction or manual to understand the parameters, please let me know.

--read-tracking Track supporting reads by qname. Increases file sizes. [off] -e, --error-rate Fractional difference two reads can have to overlap. See SGA. 0 is fast, but requires error correcting. [0]

Thank you, Sanghoon