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Old 05-24-2012, 12:50 PM   #1
bioman1
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Join Date: May 2012
Posts: 80
Default Varscan-output interpretation

Hi all,

I am new to NGS analysis. I have used bowtie (ver:bowtie-0.12.7) for aligning reference sequence (fastq format) with two paired end files of illumina reads (fastq format).
I used SAM tools (ver:samtools-0.1.18) and made a 'mpileup' file.
Then I have used Varscan (ver:.v2.2.11) for variant calling. I used "mpileup2snp" command (with default parameters) to determine SNV and for heterozygosity & homozygosity.
My basic idea is to call heterozygous SNV with conservative filters, such as coverage, variant allele
frequency, strand representation and p-value to isolate high-confidence calls.

Using the command "mpileup2snp", I got the output as follows. Given 1 column as an example
Chrom - gi|371443199|gb|JH556661.1|
Position - 2594265
Ref- G
Var- C
Cons:Cov:Reads1:Reads2:Freq:P-value- S:21:14:7:33.33%:4.3101E-3
StrandFilter:R1+:R1-:R2+:R2-val- Fail:12:2:0:7:3.096E-4
SamplesRef- 0
SamplesHet- 1
SamplesHom- 0
SamplesNC - 0
Cons:Cov:Reads1:Reads2:Freq:P-value- S:21:14:7:33.33%:4.3101E-3

1.Please let me know whether I am using the correct command to call heterzygous SNV with high-confidence calls(whether I have to use mpileup2snp or mpileup2indel or mpileup2cns?)

2.Can I parse these variant call by chromosome?. How Can I do that?

3.Is it possible to view regions of high and low heterozygosity in the genome?. If possible, how can I do that?

Thanks in advance
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