I'm in need of a practice pileup file to test a program I'm making. Is there a place to get one?

Question

[procrastrjf]

If not, is there a place where a BAM and its FASTA file can be found together? My program is designed to gather allelic frequencies from pileup files and it works well with SNPs but I need a file that has lots of different INDELs to test that part of my program. The documentation on pileup format isn't quite enough (more of the same here) because there are so few examples of INDELs and I want to put my program through the paces.

Answer 1

[Matt Shirley]

You might try sra-pileup from the NCBI SRA toolkit. You can even just use some of the examples from the documentation like:

sra-pileup -r SRR390728 > example.pileup