BWA index

[adrian]

Dear group,

Previously I used index like the following on human genome:

bwa index -a bwtsw -c Hsapiens37.fasta

I ran the subsequent analysis steps and compared the end result with others where they just used

bwa index Hsapiens37.fasta
and carried out end analysis resulting in .sam file.


now when i compare results from -a bwtsw option to no parameter indexing (2nd option), majority of reads are aligned reversed etc.

one should use this option or not?
what happns using -a bwtsw and -c and what happens if I dont.

could some one help me here. thanks
Adrian

[Chipper]

Hi, not sure I understand your question but -c is the option you use if you have SOLiD colorspace reads.

[adrian]

Thank you! i got it!

[adrian]

how much time does it normally take to index 49 fasta format chromosomes (including 24 human chrs + other contigs), If I do the following:

$ bwa index Hsapiens37.fasta

I have been running this for last 24 hours and it is till on...

$ bwa index Hsapiens37.fasta
[bwa_index] Pack FASTA... 138.06 sec
[bwa_index] Reverse the packed sequence... 37.73 sec
[bwa_index] Construct BWT for the packed sequence...

according to BWA homepage any genome that is over 4GB is cannot be index by BWA.
the genome size I am trying to index is 5.3GB. This includes all chromosomes and other 'chrN_random' and chr6 haplotypes. All these in one file is over 5 GB. Has any one successfully tried to index these using BWA.
thanks