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Hi all,
this may seem a rather odd question, I am ultimately looking to get a VCF file containing calls for all my samples in a batch of exomes.
The issue is, I want to have active reference calls for any loci that are variant in my dataset, which I would get using the mpileup command with default settings; this is so I can ensure that we do not just have no coverage in some samples in a region for example, as opposed to them being reference.
However, I do not want the statistical alterations that come with the default mpileup (i.e. upweighting of low-quality shared variants, downweighting of unique variants). I could just remove the '-v' flag, but that would give all calls for every base, which will give me huge files.
Any ideas on a way to do this? I am yet to have any ideas that do not seem hugely cumbersome.
Many thanks in advance.
this may seem a rather odd question, I am ultimately looking to get a VCF file containing calls for all my samples in a batch of exomes.
The issue is, I want to have active reference calls for any loci that are variant in my dataset, which I would get using the mpileup command with default settings; this is so I can ensure that we do not just have no coverage in some samples in a region for example, as opposed to them being reference.
However, I do not want the statistical alterations that come with the default mpileup (i.e. upweighting of low-quality shared variants, downweighting of unique variants). I could just remove the '-v' flag, but that would give all calls for every base, which will give me huge files.
Any ideas on a way to do this? I am yet to have any ideas that do not seem hugely cumbersome.
Many thanks in advance.
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