Question: Copy number variation detection
1
gravatar for v27
12 weeks ago by
v2710
v2710 wrote:

`Hi

I trying to detect copy number variation using varscan:

the command that i used is

samtools mpileup -q 1 -f Reference.fa k_output_bowtie2.bam | java -jar VarScan.v2.3.9.jar  copynumber varscan_S14 --mpileup 1

i get the following error:

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bam_pileup_core] the input is not sorted (reads out of order)
[bam_plp_destroy] memory leak: 1. Continue anyway.
Min coverage:   10
Min avg qual:   15
P-value thresh: 0.01
Reading input from STDIN
Reading mpileup input...
Parsing Exception on line:
NC_007196.1 2373565 A   1   ^9, 1
6

even when i input the sorted bam file

samtools mpileup -q 1 -f Reference.fa k14_output_bowtie2_sorted.bam |java -jar VarScan.v2.3.9.jar copynumber v1 --mpileup 1

i get an error :

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Min coverage:   10
Min avg qual:   15
P-value thresh: 0.01
Reading input from STDIN
Reading mpileup input...
Error: Invalid format or not enough samples in mpileup: NC_007194.1 80  C   0

Could anyone guide me where i am going wrong .

ADD COMMENTlink modified 12 weeks ago by d-cameron1.9k • written 12 weeks ago by v2710

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 12 weeks ago by Ram17k

thank you. I appreciate it. I will keep it in mind for the future.

ADD REPLYlink written 12 weeks ago by v2710
0
gravatar for d-cameron
12 weeks ago by
d-cameron1.9k
Australia
d-cameron1.9k wrote:

The VarScan documentation states:

copynumber
This command calls variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair.

You only have one sample ([mpileup] 1 samples in 1 input files) and VarScan copynumber requires both a tumour and a normal. This is why it's giving you the error

Error: Invalid format or not enough samples in mpileup:

You'll need to use a different tool if you want copy number data from a single sample.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by d-cameron1.9k

thank you.

I am not working on tumor data. I have a reference fungi sequence. and four other fungi samples. I have 2 objectives: to find the SNPs and second to find the copy number variation among genes.

I have successfully detected the SNPs using samtools and vcf tools.

I am stuck with detection of copy number variation.Could you suggest some tool for that.

ADD REPLYlink written 12 weeks ago by v2710
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