Hi,
I have just started using FreeBayes as a comparison to samtools as they both take BAMs and produce a VCF output which is ideal for scripting. FreeBayes actually seems like the ideal free-standing, simple and fast SNP caller I have been longing for, however the values in the VCF INFO column do not seem to match what is in the alignment.
In particular the DP value almost never seems to match what I can see in alignment viewers. It is always less than the number of reads I see stacked at the SNP position while VCFv4.1 claims that DP should represent the _total_ read depth.
Additionally, the AC (Total number of alternate alleles in called genotypes) and AN (Total number of alleles in called genotypes) values seem to almost never vary no matter what the read depth and number of alt alleles at a SNP position. To be more precise AC is always either 1 or 2 and AN seems fixed at 2 no matter what.
Is this a known quirk of FreeBayes? These are very important values that I need to parse from the VCF output but they just make no sense after having used samtools for a few years.
Thanks.
I have just started using FreeBayes as a comparison to samtools as they both take BAMs and produce a VCF output which is ideal for scripting. FreeBayes actually seems like the ideal free-standing, simple and fast SNP caller I have been longing for, however the values in the VCF INFO column do not seem to match what is in the alignment.
In particular the DP value almost never seems to match what I can see in alignment viewers. It is always less than the number of reads I see stacked at the SNP position while VCFv4.1 claims that DP should represent the _total_ read depth.
Additionally, the AC (Total number of alternate alleles in called genotypes) and AN (Total number of alleles in called genotypes) values seem to almost never vary no matter what the read depth and number of alt alleles at a SNP position. To be more precise AC is always either 1 or 2 and AN seems fixed at 2 no matter what.
Is this a known quirk of FreeBayes? These are very important values that I need to parse from the VCF output but they just make no sense after having used samtools for a few years.
Thanks.
Comment