FilterHD error

[Alxmertz]

filterHD is returning an error when I attempt to run the bias field analysis. I'm using the run-example.sh on TCGA derived data. Below the terminal output and code segment is pasted:
Code:
`

The tumor read depth is now analysed with the bias field from the matched normal. The diffusion constant is set to zero. If left free, it should converge to a very small value. The jump rate could be slightly higher. The LLH should be higher than for the run above indicating the presence of the bias field. Now we are interested in the jumps.

cmd="$filterHD --data $tumorCNA --mode 3 --pre ${results}/tumor.cna.bias --bias $bias --jumps 1"
echo $cmd
$cmd
echo

`
Terminal:
filterHD: Fitting jump-diffusion model to data at 129 loci in 23 segment(s) in 1 sample(s) with a poisson emission model:
ERROR 1 in get_bias()
24 2792295 1.70e+02 9.81e+01 0.00e+00

./build/filterHD --data ./cloneHDdata/tumor.baf.txt --mode 1 --pre ./cloneHDresults/tumor.baf --jumps 1 --reflect 1 --dist 1

[ivazquez]

Hi @Alxmertz,

I think the issue you are running into is that your ${tumorCNA} file does not contain the same number of chromosomes as your ${bias} file. You are probably missing chr Y/chr 24 in ${tumorCNA}.

This throws an error because doing bias correction of tumour read depth requires a corresponding matched normal on every chromosome, and typically there is sufficient coverage across both samples on all chromosomes. I hope that fixes it!

Ignacio