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  • Indexing Varscan vcf output

    Hi,

    The current version of Varscan (2.3.4) is still producing non-compliant vcf output.

    Does anyone have/know of a way of getting the output into a state where it can be properly indexed by IGV (using IGVtools, based on GATK API) for viewing?

    Many thanks,
    Nestor

  • #2
    To (partially) answer my own question, tabix appears less fussy than igvtools in producing an index sufficient to keep IGV happy, once non-compliant indel coding and other formatting issues have been addressed (or at least glossed over ).

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    • #3
      Originally posted by NestorNotabilis View Post
      To (partially) answer my own question, tabix appears less fussy than igvtools in producing an index sufficient to keep IGV happy, once non-compliant indel coding and other formatting issues have been addressed (or at least glossed over ).
      Indeed, I was about to comment 2.3.4 works fine in my hands for VCF generation but I index with tabix routinely and not IGV. A welcome relief from having to massage the VarScan output every time.

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