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  • variant calling from pacBio Sequel data

    I am struggling with variant calling in 'Re-sequencing' mode using SMRT v4 and so far found that the VCF format generate by SMRTv4 is not valid.
    Their VCF v3.3 is a non-documented weird version which does not validate and includes strange annotations (I&D for INS and DEL and not reporting the last conserved base in INS calls - among probably other weirdnesses).

    The PB GFF output is not very helpful either as I need to compare variants with other public and platform results (I need VCF4)

    * Does anyone map Sequel reads to a reference assembly using external software and leading to VCF 4 results ?

    * Does anyone have success calling variants from PacBio re-sequencing:BAM alignments and corresponding reference fasta assembly using other tools?

    If yes please let us know which.
    Thanks in advance.

    ref: http://seqanswers.com/forums/showthread.php?t=34201
    Last edited by splaisan; 03-25-2017, 06:29 AM.
    http://www.bits.vib.be/index.php

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