Hi!
I'm trying to use XHMM for CNV detection but I have a few problems:
1) I'm following this quide http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml for the use and I installed PLINK/Seq tools but when I try to use:
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:
I delete the second --ecludeTargets low_complexity_targets.txt but in the next step I have problem with runs PCA on mean-centered data:
but this is the error:
So I tried to bypass this step too but then I have an error on discovers CNVs in normalized data:
Anyone can help me?
Thanks in advance.
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.
I'm trying to use XHMM for CNV detection but I have a few problems:
1) I'm following this quide http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml for the use and I installed PLINK/Seq tools but when I try to use:
Code:
"./sources/scripts/interval_list_to_pseq_reg EXOME.interval_list > ./EXOME.targets.reg"
2) I tried to bypass PLINK/Seq step so in this command for filters samples and targets and then mean-centers the targets:
Code:
./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
Code:
"./xhmm --PCA -r ./DATA.filtered_centered.RD.txt --PCAfiles ./DATA.RD_PCA"
Code:
ERROR: Unable to read header line from input stream
Code:
ERROR: Unable to read header line from input stream
Thanks in advance.
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.