Are default kernels available for the rest of the markers?

[Emma-M-Rath]

Hi, I am not able to get the first Iteration 0 to run for computePnSlippageDefault. I am able to run the default kernel for 8779 markers on chr21, to completion, and obtain a vcf output. Do you have the default kernel available for the other chromosomes, and for the panel markers, and for the rest of the markers on chr21?

[snaedis88]

Hi Emma.
You don't need to run computePnSlippageDefault on other regions than the chr21 kernel. You can use the per sample slippage rates it generates as input for genotyping the other regions on chr21 and the other chromosomes. You need to run computeReadAttributes for those regions and then msGenotyperDefault using paths to the attributes from computeReadAttributes and the slippage rates from computePnSlippageDefault.
Hope this helps and if anything is unclear, please don't hesitate to comment again.

Best,
Snædís

[Emma-M-Rath]

Hi Snædís, Thank you very much for this prompt and helpful information :) However, when I run computePnSlippageDefault on only 2 of chr21 markers (or other chromosome markers), after printing out "Finished reading PnList.", it hangs as if it is in an infinite loop.