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I am running bcftools consensus on a series of genomic regions (fasta), by applying variants from a single subject and getting IUPAC codes as output ( -s -H I ).
For overlapping variants, now I am getting two kinds of warnings -
1) "The site chr[..]:[..] overlaps with another variant, skipping..."
and
2) "Warning: ignoring overlapping variant starting at chr[..]:[...]"
More specifically, suppose I have two regions - chr1:100-200, and chr1:300-400 (just using these small coords as example):
bcftools consensus run on the first region will output only warnings of type 1).
when running consensus on the second region, I get the warning 2) for positions belonging to the first region (chr1:100-200), then the usual warning 1) for positions within the actual region being processed (chr1:300-400).
In this example, the vcf used for both regions would be the same and have variants spanning both intervals (chr1:100-400).
I am used to the warning 1) since previous versions of bcftools, but kind of confused by the warning 2) - since it considers earlier variants.
Just wondering if you have an explanation for this behavior - hopefully not a bug?
The two warnings are emitted from two slightly different contexts. The code is a bit opaque, so it's hard to tell without seeing specific examples, but the difference should be harmless.
Hello,
I am running bcftools consensus on a series of genomic regions (fasta), by applying variants from a single subject and getting IUPAC codes as output ( -s -H I ).
For overlapping variants, now I am getting two kinds of warnings - 1) "The site chr[..]:[..] overlaps with another variant, skipping..." and 2) "Warning: ignoring overlapping variant starting at chr[..]:[...]"
More specifically, suppose I have two regions - chr1:100-200, and chr1:300-400 (just using these small coords as example):
In this example, the vcf used for both regions would be the same and have variants spanning both intervals (chr1:100-400).
I am used to the warning 1) since previous versions of bcftools, but kind of confused by the warning 2) - since it considers earlier variants.
Just wondering if you have an explanation for this behavior - hopefully not a bug?