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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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scan_region.pl #56

Open hui-1 opened 4 years ago

hui-1 commented 4 years ago

hi , when i did cnv annotation ,the code was scan_region.pl sampleall.cnv hg19_refGene.txt -refgene > sampleall.cnv.rg19, the reflink file can not find in ucsc now, the annotation result only show the NM_022463 id ,not the gene name, i don't know the reason,how can i get the annotation gene name by scan_region.pl?
hope for your reply! thanks

kaichop commented 4 years ago

There is an argument (probably -gene2) that you can use to take gene name from the refGene.txt file directly.

On Wed, May 20, 2020 at 9:50 AM hui-1 notifications@github.com wrote:

hi , when i did cnv annotation ,the code was scan_region.pl http://scan_region.pl sampleall.cnv hg19_refGene.txt -refgene > sampleall.cnv.rg19, the reflink file can not find in ucsc now, the annotation result only show the NM_022463 id ,not the gene name, i don't know the reason,how can i get the annotation gene name by scan_region.pl? hope for your reply! thanks

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hui-1 commented 4 years ago

Thank you very much，you are so kind! it is an argument( --name2_flag )，Thanks again for your reminding.