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 .
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.