Question: How does WGS normalization perform between samples
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gravatar for bxia
2.3 years ago by
bxia150
bxia150 wrote:

I am currently using whole genome sequencing to identify structure variation (SV)

I wonder whether I need to perform normalization between the samples.

For example,

2-micron 10 1 N <dup> . . SVTYPE=DUP;STRANDS=-+:155;SVLEN=6307;END=6317;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=155;PE=0;SR=155 GT:SU:PE:SR ./.:111:0:111 ./.:44:0:44

There are 155 SR split reads support this SV.

But it appeared in both treatment and control. If I call the SV separately for treatment and control, there is 111 SR for treatment, 44 for control.

Does Lumpy perform some normalization for calling the SV? such as total reads normalization?

Thanks,

whole genome sequencing • 643 views
ADD COMMENTlink written 2.3 years ago by bxia150

Lumpy takes care of that internally. What you have to do is to filter out if a SV is germline or somatic. See here for example.

ADD REPLYlink written 2.3 years ago by ATpoint36k
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