`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 .
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.
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.
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