When I only have two samples,such as two bam file ,how can I use XHMM to find CNV ?
0
0
Entering edit mode
7.3 years ago

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 • 1.9k views
ADD COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode

Thank you!

I have changed to use CNVnator instead.

ADD REPLY

Login before adding your answer.

Traffic: 2108 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6