Hi! I'm trying to use XHMM for CNV detection but I have a few problems:

1) I'm following this quide [url]http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml[/url] for the use and I installed PLINK/Seq tools but when I try to use:

"./sources/scripts/interval_list_to_pseq_reg EXOME.interval_list > ./EXOME.targets.reg"

there is no file or script like interval_list_to_pseq_reg. So I saw in the plinkseq directory plinkseq/sources but there isn't any directory script, how can I fix it?

2) I tried to bypass PLINK/Seq step so in this command for filters samples and targets and then mean-centers the targets:

./xhmm --matrix -r ./DATA.RD.txt --centerData --centerType target \
    -o ./DATA.filtered_centered.RD.txt \
    --outputExcludedTargets ./DATA.filtered_centered.RD.txt.filtered_targets.txt \
    --outputExcludedSamples ./DATA.filtered_centered.RD.txt.filtered_samples.txt \
    --excludeTargets ./extreme_gc_targets.txt --excludeTargets ./low_complexity_targets.txt \
    --minTargetSize 10 --maxTargetSize 10000 \
    --minMeanTargetRD 10 --maxMeanTargetRD 500 \
    --minMeanSampleRD 25 --maxMeanSampleRD 200 \
    --maxSdSampleRD 150

I delete the second --ecludeTargets low_complexity_targets.txt but in the next step I have problem with runs PCA on mean-centered data:

"./xhmm --PCA -r ./DATA.filtered_centered.RD.txt --PCAfiles ./DATA.RD_PCA"

but this is the error:

ERROR: Unable to read header line from input stream

So I tried to bypass this step too but then I have an error on discovers CNVs in normalized data:

ERROR: Unable to read header line from input stream

Anyone can help me?

Thanks in advance.