Understanding BAM format.

[Joker!sAce]

Hi,

I have this output in BAM format.

NA06984-SRR006041.1145152 1040 1 113040605 57 325M * 0 0 TTGATCACTTCACACACATCTTCATCGATGAGGCTGGCCA
CTGCATGGAGCCTGAGAGTCTGGTAGCTATAGCAGGTGAGGGACTCAGGTGGGGCTGCAGGTATACACCCTGTGTGGGTCAGAGAGGTTGCACCACTTACCTTTCTTCCCACACCTCTTCTGCTTCCCAGGGCTGATGGAAGTA
AAGGAAACAGGTGATCCAGGAGGGCAGCTGGTGCTGGCAGGAGACCCTCGGCAGCTGGGGCCTGTGCTGCGTTCCCCACTGACCCAGAAGCATGGACTGGGATACTCACTGCTGGAGCGGCTGCTCACCTACAACTCCCTG 7
99::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::88:::::::::::;;;;;;;;;;;;;::888:;;;;;;;;;;;;;;;;;;;;;;;;;;
;;888;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;:9::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;::::;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;::::::::::::::::::::::::: RG:Z:SRR006041 NM:i:0

(This is data from the 1000 genomics project.)

I'm constructing a pipeline to study variations (I get fast-q sequence, index it, align it to ref.seq hg18, do a couple of format conversions and get BAM, call indels and snps, add them to a db, call larger variations, look if they've been reported before, give out fancy graphs and charts, display the alignment, submit a report).

I'm learning about BWA aligner and the BAM format right now. I'm using pilot data on un-aligned sequences from the 1000 genomes project (because I will have similar BAM outputs).

I have to study and make sense out of this BAM format. I've read this tutorial on understanding the SAM/ BAM format with little help. Could someone give me further pointers?

Thanks a lot!
Joker!sAce

[nilshomer]

What specific questions about the format do you have?

[Joker!sAce]

I understand that there are a lot of columns in this record.

NA06984-SRR006041.1145152
1040
1
113040605
57
325M
*
0
0
TTGATCACTTCACACACATCTTCATCGATGAGGCTGGCCACTGCATGGAGCCTGAGAGTCTGGTAGCTATAGCAGGTGAGGGACTCAGGTGGGGCTGCAGGTATACACCCTGTGTGGGTCAGAGAGGTTGCACCACTTACCTTTCTTCCCACACCTCTTCTGCTTCCCAGGGCTGATGGAAGTAAAGGAAACAGGTGATCCAGGAGGGCAGCTGGTGCTGGCAGGAGACCCTCGGCAGCTGGGGCCTGTGCTGCGTTCCCCACTGACCCAGAAGCATGGACTGGGATACTCACTGCTGGAGCGGCTGCTCACCTACAACTCCCTG
799::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::88:::::::::::;;;;;;;;;;;;;::888:;;;;;;;;;;;;;;;;;;;;;;;;;;;;888;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;:9::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;::::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;:::::::::::::::::::::::::
RG:Z:SRR006041
NM:i:0

I'd like to know what they mean. I do have faint ideas but I'd like to know about it anyways.

[krobison]

You'll get much better answers if you post specific questionswhich can't be easily found in the SAM format documentation.

[Joker!sAce]

My study involves divergence study on the gene p53 on short arm of chromosome 17. I need to extract this part of the sequence.

I understand that I can do this in two ways:
1. Get raw fasta reads.
2. Extract from the aligned(to hg18) data(in BAM format).

How do I do it the 2'nd part?

[krobison]

If you know the chromosomal coordinates for your gene (which you can find in the UCSC files or via the browser), then SAMtools can extract this efficiently

[Joker!sAce]

This sequence has been aligned to hg18. I know the chromosomal co-ordinates for hg18 (chr17:7,520,037-7,531,588 - That's the tp53 repressor gene)

How do I proceed from here?

[krobison]

samtools view aligned.bam chr17:7520037-7531588 > tp53.sam