I am preparing to order barcoded primers for a sequencing project on the PGM, and would appreciate some feedback on the options for data analysis before I make this purchase. We are sequencing 4 loci in approximately 65 individuals (diploid, mammal, WGS available). The amplicons will be ~350 bp. We were told this could be done on a single 314 chip.
We are going through a sequencing center, so I do not have access to the Ion Torrent server. If I understand correctly, I could pay to use the Variant Caller through Amazon though. What are the general costs? Does this work when not using the human genome as a reference?
Does anyone have experience with any free programs for variant analysis of PGM data? How about GATK? I hear so much about the need to stick with platform-specific analyses to deal with their particular types of sequencing errors, and just wanted to know what the general thoughts were on that topic.
We are going through a sequencing center, so I do not have access to the Ion Torrent server. If I understand correctly, I could pay to use the Variant Caller through Amazon though. What are the general costs? Does this work when not using the human genome as a reference?
Does anyone have experience with any free programs for variant analysis of PGM data? How about GATK? I hear so much about the need to stick with platform-specific analyses to deal with their particular types of sequencing errors, and just wanted to know what the general thoughts were on that topic.
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