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When I only have two samples,such as two bam file ,how can I use XHMM to find CNV ?

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 thanks!

lianhe

xhmm cnv
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updated by Ram Ram • written by zhaolianhe1992 • zhaolianhe1992

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."

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written by h.mon h.mon

Thank you!

I have changed to use CNVnator instead.

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written by zhaolianhe1992 • zhaolianhe1992

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