Hello all,
I used to be able to use CLC for my SNP calling, which generates the reference base and the frequency of the variant allele in separate columns. I no longer have access to this program and have been using bwa-samtools. I have all of my files in bam format and have been generating SAM pileup tables using the -vcf option. The problem is it gives you the variant allele and consensus allele (not reference allele) and the phred scaled quality of the SNP, not its frequency. Is there a better software to use in order to get this information? Or is there a way to get this information from samtools?
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I used to be able to use CLC for my SNP calling, which generates the reference base and the frequency of the variant allele in separate columns. I no longer have access to this program and have been using bwa-samtools. I have all of my files in bam format and have been generating SAM pileup tables using the -vcf option. The problem is it gives you the variant allele and consensus allele (not reference allele) and the phred scaled quality of the SNP, not its frequency. Is there a better software to use in order to get this information? Or is there a way to get this information from samtools?
sasignor is online now Report Post Edit/Delete Message
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