Saturday, February 15, 2014

BWA vs. SNAP

Goal

Compare BWA to SNAP

Approach





Preparation

#app


#data, simulated from hg19-chr20, paired, 30x average coverage
$wgsim -N 10000000 -r 0.01 -1 100 -2 100 -S11 -e0 chr20.fa A1.fq A2.fq > mut.txt



Running Time




BWA SNAP
30m20s 20m01s



Mapping metrics





Variants Concordance





Impression (so far)


1) SNAP is 1.5x faster than BWA (memory consumption is not evaluated)
2) SNAP aligned more TP alignments, less FP alignments than BWA
3) SNAP generated more TP (8512 vs. 740) and FP (2715 vs. 596) variants than BWA






1 comment:

  1. Was this using bwa sw, aln, backtrack, or mem?

    ReplyDelete