/FixMultiInDel

Fix the multiallelic indels from haplotypecaller to deal with bug with overlapping in/dels

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FixMultiInDel

Fix problem with VCF calls multiple insertion and/or deletion events at a given position. Uses bcftools norm to do the splitting.

Examples:

  • From haplotype
    5   112174757   .   GAAGA   G,GGA
  • after bcftools norm -m-
    5   112174757   .   GAAGA   G
    5   112174757   .   GAAGA   GGA
  • after normalizeInDels.py
	5	112174757	.	GAAGA	G
	5	112174757	.	GAA		G