How to annotate Copy Number Variations (Output of VarScan2)

Question

[Raheleh]

Hi,

I ran this command:

samtools mpileup -q 1 -f hg38.fa normal.sorted.bam tumor.sorted.bam | java -jar VarScan.v2.4.3.jar copynumber varScan --mpileup 1

and this is a part of the output:

> chrom  chr_start  chr_stop  num_positions  normal_depth  tumor_depth  log2_ratio  gc_content
> chr1  13217   13316   100     17.4     14.1   -0.301  61
> chr1  13317   13395   79      18.3     13.3   -0.458  53.2
> chr1  65848   65942   95      10.7     2.5    -2.1    44.2

I searched a lot to see how can be annotated but no success yet. Can any one suggest any tools to annotate this CNV output?

Many thanks!

[brunobsouzaa]

Did you solved your problem?

[Kevin Blighe]

Look at the answer below.

Answer 1

[Pierre Lindenbaum]

first idea: use bedtools intersect with a bed file chrom/start/end/gene to see if those positions intersect with a gene...