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Old 05-25-2016, 04:49 AM   #1
Location: Italy

Join Date: Nov 2015
Posts: 18
Unhappy XHMM and Ion Torrent

I'm trying to use XHMM to detect CNV with BAM files from PGM Ion Torrent. I'm using the guide on but I have some problems.

I tried to use the example files to learn the pipeline and I used the reference genome hs37 (I downloaded it from and I obteined the output with success. So I tried to use XHMM with my BAM (2 group of 6 and 7 BAM each) files and for the first step (coverage and depth analysis) I can't use the hs37 reference genome because the program return this error:

##### ERROR MESSAGE: Badly formed genome location: Contig 'chr17' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

For this step I tried to use two different exome.interval_list file in 2 different format:
1) 13:32900238-32900287
2) chr13:32889617-32889804

but in both of cases the error was the same.

So I tried to use GRCh37.p13.genome for reference genome with the exome list in format chr13:32889617-32889804. Is it correct?

If I use the GRCh37.p13 reference genome I can continue the analysis but when I have to do the
"Filters samples and targets and then mean-centers the targets" step if I use the parameters on the guide I get an empty file, so I tried to modify the parameters, in particular "maxMeanSampleRD" but even if I see my positive patient (with the CNV) in the file (DATA.filtered_centered.RD.txt) my final output file (DATA.xcnv) is empty (so I can't see my CNV). How can I resolve? Where am I wrong?

I see that the example BAM files are from Illumina but I use PGM Ion Torrent with amplicon's kit. Is it a problem for the analysis?

I make so many attempts and, if I don't wrong, my problem is on two particular filters: target and sample. Is there any hint for this problem?

I apologize for the questions but this is my first time with the real work as a bioinformatic so I'm so inexperienced.

Thank you in advance for the answers.
PandoraMid is offline   Reply With Quote
Old 05-25-2016, 05:16 AM   #2
Senior Member
Location: UK

Join Date: Jan 2010
Posts: 390

Cross-posted to the XHMM User Group:
Bukowski is offline   Reply With Quote

cnv, ion torrent, xhmm

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