Varscan-SNV identification

[bioman1]

Dear 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). Then 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 "pileup2snp' command (with default parameters) to determine SNV and for heterozygosity & homozygosity.

1. The output gives in colums and I have below as rows for easy reading
Output:
Chrom:gi|53564564|gb|JH556356.3
Position:1781287
Ref:T
Cons:Y
Reads1:7
Reads2:2
VarFreq:22.22%
Strands1:2
Strands2:2
Qual1:27
Qual2:26
Pvalue:0.98
MapQual1:1
MapQual2:1
Reads1Plus:5
Reads1Minus:2
Reads2Plus:1
Reads2Minus:1
VarAllele:c


2. Any any one can tell me how identify SNV (how many of them are heterzygous & homozygous) with the above output ?. I have searched this forum, I could not find any help.

[paolo.kunder]

have a look to the user manual,

http://varscan.sourceforge.net/using-varscan.html

for instance:

The output gives in colums and I have below as rows for easy reading
Output:
Chrom:gi|53564564|gb|JH556356.3 >> chr of interest
Position:1781287 >> position
Ref:T >> reference base
Cons:Y >> check http://www.ensembl.org/info/website/glossary.html ( Y means your base changed form T to C
Reads1:7 >> reads supporting base T
Reads2:2 >> reads supporting base C
VarFreq:22.22% >> frequency C/T 2/7 =22,22
Strands1:2
Strands2:2
Qual1:27
Qual2:26
Pvalue:0.98
MapQual1:1
MapQual2:1
Reads1Plus:5
Reads1Minus:2
Reads2Plus:1
Reads2Minus:1
VarAllele:c

concerning heterzygous & homozygous you should check VarFreq.

pk

[bioman1]

Varscan SNV

thanks a lot for suggestion. Do you know how to view regions of high and low heterozygosity in the genome. Is it through genome browsers?. If so, can you suggest any genome browsers.

[giuliano stirparo]

You could upload your VCF file in IGV 2.1