Basic statistics from alignment using bwa

[bioinf newbie]

Hi
1. If you are going with a standard tool like GATK they have specifications and a resource bundle: http://gatkforums.broadinstitute.org...lic-ftp-server from where you can download the reference genome.
2. to get basic stats-- i suggest samtools flagstat, idxstats. You can also check Picard tools and GATK .
3. yes, to know more about what flagstat output means, you can refer: http://samtools.sourceforge.net/SAM1.pdf

[NGS_New_User]

Hi everyone,

I have a couple of questions that I am sure most of you are already good at. I searched the forum but haven't seen similar questions, but if anyone can lead me to a similar solved thread with the same issue, I will be grateful.

My first question stems from this: I downloaded the reference hg19 and concatenated the chr*.fa files. Do I need to concatenate only chr1-22, chr X,Y,M then ignore the chrUn_gl*.fa and chr*_random.fa? Or should I concatenate all the chr files regardless.
I read somewhere that when concatenating the files should be arranged in order. Is that necessary, and if so how does one arrange the unknown and random chr files in order?

My other question is, I am trying to retrieve some basic statistics from my alignment that I did using bwa. I need to get basic stats eg number of reads mapped, average coverage etc

Which tools should I use to get such statistical info?

I am a newbie in this area and I am not sure I am doing this right. I used samtools flagstat and I got this:

308846 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
270177 + 0 mapped (87.48%:nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (nan%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (nan%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)