Indexing Varscan vcf output

[NestorNotabilis]

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

[NestorNotabilis]

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 ).

[Bukowski]

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.