add reference fasta sort fix

[arundurvasula]

for i in `seq 1 12`; do samtools faidx ref.fa $i >> sorted_ref.fa; done

Then gzip your fasta and run

samtools faidx sorted_ref.fa.gz

to get your .fai file.

[tvkent]

this was bc ref fastas weren't working if the chromosomes were out of order

[arundurvasula]

Added to FAQ