XHMM and PLINK/Seq problem

Question

[martyferr90]

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.

[martyferr90]

UPDATE:

I managed to run the program, and I understand where was the error. In the filtered step, with those parameters, the output file was empty, so I tied to modify the value, in particular minMeanSampleRD. But ther's one more problem. I'm using a known set of BAM files, in which i know who have a CNV, but even if I don't see an error anymore the final step (when I produce the xcnv file) produce an empty file.

I use PGM Ion Torrent with amplicon's kit.

Anyone can help me?

Thanks in advance.

Answer 1

[mtkk94]

"./sources/scripts/interval_list_to_pseq_reg

This is present in XHMM and not in plink. Try finding it in "XHMM/sources/scripts/interval_list_to_pseq_reg" XHMM folder.