Question: When I only have two samples,such as two bam file ,how can I use XHMM to find CNV ?
gravatar for zhaolianhe1992
5.1 years ago by
zhaolianhe199220 wrote:

hi all ,

I use two bam file to find CNV, the software is XHMM, but the result .xcnv is always empty,

However the example have 30 bam files and they give a good result .

I want to know if XHMM needs a certain number of examples to produce cnv results.


Many thnks!


xhmm cnv • 1.4k views
ADD COMMENTlink written 5.1 years ago by zhaolianhe199220

You should look for an appropriate tool for the dataset you have. From XHMM manual:

"XHMM was explicitly designed to be used with targeted exome sequencing at high coverage (at least 60x - 100x) using Illumina HiSeq (or similar) sequencing of at least ~50 samples. However, no part of XHMM explicitly requires these particular experimental conditions, just high coverage of genomic regions for many samples."

ADD REPLYlink written 5.1 years ago by h.mon31k

Thank you!

I have changed to use CNVnator instead.

ADD REPLYlink written 5.1 years ago by zhaolianhe199220
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