Annotation for copy number called segments from VarScan 2 output.
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2.2 years ago
TanayB • 0

Hi

I have used VarScan 2 to call Copy Number Alterations from tumor WES data (200x covearge). I have generated the output using mergeSegments.pl script and the output looks like this:

chrom chr_start chr_stop seg_mean num_segments num_markers p_value event_type event_size size_class chrom_arm arm_fraction chrom_fraction

chr1 12932 777753 -1.60998 5 136 0.000932487891761 deletion 764822 focal chr1p 0.61% 0.31% chr1 803673 809652 -0.656233333333333 3 17 1.56428608479339E-08 deletion 5980 focal chr1p 0.00% 0.00% chr1 866185 874737 -0.3728 1 18 1.31976726525566E-10 deletion 8553 focal chr1p 0.01% 0.00%

Now, I am wondering how could I do further analysis using the called copy number segments? How to annotate the genes from the called segments? Also, is there a way to represent a plot with this file because the plots generated after segmentation using DNACopy library looks noisy which I have also attached All chromosome plots Chromosome 1 plot chr8.

The authors have mentioned in VarScan2 paper about two files (cytoBand.txt and refGene.txt files) which were used to annotate the output file. I have used cytoBand.txt while using mergeSegmentss.pl script. I am wondering how to proceed further with this file.

Please suggest how to annotate the segments with gene names that are amplified or deleted in my samples. Thank you.

Annotation Copy VarScan2 Segmentation CNVs Number • 500 views
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