Hello all,
I'm new to bioinformatics and I'm trying to teach myself most of these things.
I just called snp's with samtools and mpileup. I then proceeded to filter using:
bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf
I'm a bit confused on why I should worry about filtering on *maximum* read depth rather than on minimum. Shouldn't I select a minimum read depth and allow for the maximum to go as high as possible? Could this lead to other sorts of trouble?
Thanks for help or redirecting me to the proper source,
Eric,
I'm new to bioinformatics and I'm trying to teach myself most of these things.
I just called snp's with samtools and mpileup. I then proceeded to filter using:
bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf
I'm a bit confused on why I should worry about filtering on *maximum* read depth rather than on minimum. Shouldn't I select a minimum read depth and allow for the maximum to go as high as possible? Could this lead to other sorts of trouble?
Thanks for help or redirecting me to the proper source,
Eric,
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