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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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VarScan VCF file deletion contains "-" in Alt field #507

Closed tedtoal closed 7 years ago

tedtoal commented 7 years ago

VarScan (v 2.4.2) uses the invalid Alt field character "-" to signify a deletion, as in Ref=C, Alt= -T, which should instead show two Ref bases and only the T as the Alt base. I was surprised that bcftools (v 1.3.1) did not fix this.

pd3 commented 7 years ago

I am closing the issue, please see https://github.com/samtools/bcftools/issues/506 for discussion