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Output the top two haplotypes as a variant call by running smith-waterman alignment against the reference and calling any difference as variation. This is the first verion that runs end-to-end by taking in reads as bam file and writing out variant calls in VCF.

This commit is contained in:
Ryan Poplin 2011-08-24 15:18:44 -04:00
parent f37875600a
commit e5008aba00
1 changed files with 2 additions and 1 deletions
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3
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -209,6 +209,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/**
* the complete constructor. Makes a complete VariantContext from its arguments
* This is the only constructor that is able to create indels! DO NOT USE THE OTHER ONES.
*
* @param source source
* @param contig the contig
@ -293,7 +294,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
}
/**
* Create a new variant context without genotypes and no Perror, no filters, and no attributes
* Create a new variant context with genotypes but without Perror, filters, and attributes
*
* @param source source
* @param contig the contig