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
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
