Java Fasta Reference Iterator

Question

[Johan]

I'm looking for a java class/package iterate over the loci in a fasta reference and provide the read pileup at each locus from a corresponding bam file. Basically I'm looking for something like the GATK locus walker, but I don't want to use the map/reduce methodology. I've been googling, but I can't seem to find anything which fits the description. I thought that the might be something in Picard, but I can't spot how to do it. Any thing like this out there? I just want to be sure about this before I go into writing a parser of my own.

Answer 1

[Pierre Lindenbaum]

have a look at picard: SamLocusIterator and example in

• snp calling - filter reads according to quality of 5 flanking bases
• using Picard to get the depth at a given position: