bwa alignment failed

[CTGF]

Hello, I am trying to align my Illumina hiseq data using bwa:

./bwa index -c -a bwtsw -p hg19 hg19.fa

./bwa aln -t 4 -c hg19 quatrim.fq > quatrim.sai

./bwa samse -f quatrim.sam hg19 quatrim.sai quatrim.fq

Then .sam was convered to .bam

I used samstool to check the alignment:

./samtools idxstats quatrim.bam

chr1 249250621 1 0
chr2 243199373 0 0
chr3 198022430 2 0
chr4 191154276 1 0
chr5 180915260 1 0
chr6 171115067 0 0
chr7 159138663 0 0
chr8 146364022 1 0
chr9 141213431 0 0
chr10 135534747 0 0
chr11 135006516 1 0
chr12 133851895 0 0
chr13 115169878 0 0
chr14 107349540 1 0
chr15 102531392 0 0
chr16 90354753 0 0
chr17 81195210 0 0
chr18 78077248 0 0
chr19 59128983 3 0
chr20 63025520 1 0
chr21 48129895 0 0
chr22 51304566 0 0
chrX 155270560 0 0
chrY 59373566 0 0
chrM 16571 0 0
* 0 0 3081338

When I ran the above steps, everything looked fine. The quality scores of the reads are also very good. I blasted some, and they mapped perfectly to the genome. I am wondering which step(s) might have problems. Thanks!

[Bukowski]

bwa aln -c is for colorspace data (i.e. from SOLiD platforms). As is bwa index -c

You state you have Illumina data.

I suggest removing the -c options from both commands.