I get a bit confused about the mrCaNaVaR output. The "out_prefix.copynumber.bed" file tells me the copy number of each segment but it does not tell me which segment is a copy number variation region.
If I want to know which regions are CNVs, do I look at the "IS_CONTROL" column in other output files such as the "cw_norm.bed", "sw_norm.bed", or "lw_norm.bed"? The CNVs will be the "N" rows, correct? With cw_norm, sw_norm, and lw_norm, which file shold I consider when I try to find the CNV region?
Thank you for your help!
Stella
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I get a bit confused about the mrCaNaVaR output. The
"out_prefix.copynumber.bed" file tells me the copy number of each segment
but it does not tell me which segment is a copy number variation region.
If I want to know which regions are CNVs, do I look at the "IS_CONTROL"
column in other output files such as the "cw_norm.bed", "sw_norm.bed", or
"lw_norm.bed"? The CNVs will be the "N" rows, correct? With cw_norm,
sw_norm, and lw_norm, which file shold I consider when I try to find the
CNV region?
Hi Dr. Alkan,
I get a bit confused about the mrCaNaVaR output. The "out_prefix.copynumber.bed" file tells me the copy number of each segment but it does not tell me which segment is a copy number variation region.
If I want to know which regions are CNVs, do I look at the "IS_CONTROL" column in other output files such as the "cw_norm.bed", "sw_norm.bed", or "lw_norm.bed"? The CNVs will be the "N" rows, correct? With cw_norm, sw_norm, and lw_norm, which file shold I consider when I try to find the CNV region?
Thank you for your help!
Stella
you are using an obsolete version. mrcanavar moved to github a long time
ago: https://github.com/BilkentCompGen/mrcanavar
it will output .dups.bed and .dels.bed that correspond to the CNV regions.
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On Sat, Oct 7, 2017 at 9:56 AM, TzuHsueh_Huang stellathhuang@users.sf.net
wrote:
Thank you for your reply!!
Tzu-Hsueh