Hi all,
I have aligned illumina reads to the reference genome using bowtie and then created mpileup file using sam tools. I have used varscan to call variants (SNPS) using mpileup2snp with min coverage 20, min reads2 4, min avg qual 20 and p-value 0.1 settings.I would like to determine heterozygosity & homozygosity.
I get output from the varscan for some of the contigs repeated more than once showing showing different p-values, var frequency , strand filter, sample homo & sam hetero. I have counted the snps for each contig which shows strand filter-Pass. But I am confused how can i get p-value, var freq for each contig (if it is repeated more than twice)
Is there any way filter the result in varscan to get values for each unique contig?
I have aligned illumina reads to the reference genome using bowtie and then created mpileup file using sam tools. I have used varscan to call variants (SNPS) using mpileup2snp with min coverage 20, min reads2 4, min avg qual 20 and p-value 0.1 settings.I would like to determine heterozygosity & homozygosity.
I get output from the varscan for some of the contigs repeated more than once showing showing different p-values, var frequency , strand filter, sample homo & sam hetero. I have counted the snps for each contig which shows strand filter-Pass. But I am confused how can i get p-value, var freq for each contig (if it is repeated more than twice)
Is there any way filter the result in varscan to get values for each unique contig?
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