search

daviesdrew / variantcalling

0 stars 0 forks source link

BWA index "`-a bwtsw' does not work for short genomes" #16

Open peterk87 opened 4 years ago

peterk87 commented 4 years ago

Usage info for BWA index mentions "-a bwtsw' does not work for short genomes, while-a is' and a div' do not work not for long genomes".

It may be best to leave the -a as auto, which I'm assuming selects the appropriate BWT algorithm given the input sequence size.

Full BWA index usage info below:

$ bwa index

Usage:   bwa index [options] <in.fasta>

Options: -a STR    BWT construction algorithm: bwtsw, is or rb2 [auto]
         -p STR    prefix of the index [same as fasta name]
         -b INT    block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.*

Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
         `-a div' do not work not for long genomes.