wrong numbers with some BAMs

[darked89]

I got bizarre looking numbers for coverage on just single BAM file (one line of the output):

1|F0008AAR.2 998 999 A 50 50 0 140735599270096 140435982010547 1 140435981676544 67669007 636900700782336 1931 219043332221 532575944795 472446402792 . 140735561305050 140435982010544 1 140435981676544 67668767 636900700782336 795 219043332109 532575944795 472446402679 . 37965046 3 0 0 240 0 1136 112 0 113 . 140735561305050|795|37965046|1136,140435982010544|219043332109|3|112,1|532575944795|0|0,140435981676544|472446402679|0|113,67668767|.240|.,.|.

No idea why. Linux, piledriver git cloned on 2013.07.15, gcc 4.4.2.

Darek

[arq5x]

This seems like overflow. What is the actual depth at this position? Also, are you using a 32 or 64 bit machine?

[darked89]

Dear Aaron,

thanks for a quick response. If we manage to get it to work it will save me a lot of time...

I am on 64bit. I extracted the reads for the first 200bp:

samtools view -H 1991_AXE_600.R1.coral_13_r5.fq.Ld2.srma.sorted.bam > dkedra_test.sam bamtools filter -region '1|FR799588.2:1..200' -in 1991_AXE_600.R1.coral_13_r5.fq.Ld2.srma.sorted.bam | samtools view - >> dkedra_test.sam  samtools view -buS dkedra_test.sam -o dkedra_test.bam

then run: ./bin/bamtools piledriver -fasta Ld_genome_20120113.fa -in dkedra_test.bam  >  dkedra_test.piledriver.out

I can give you the genome, but you can also get the FR799588.2 quite easily, I hope. Just rename the fasta header to "1|FR799588.2"

Let me what can I do to help you solve it,

Darek Kedra

---

From: Aaron Quinlan [email protected] To: arq5x/piledriver [email protected] Cc: Darek K. [email protected] Sent: Wednesday, July 17, 2013 3:41 PM Subject: Re: [piledriver] wrong numbers with some BAMs (#2)

This seems like overflow. What is the actual depth at this position? Also, are you using a 32 or 64 bit machine? — Reply to this email directly or view it on GitHub.

[darked89]

I managed to solve the problem by upgrading to Debian 7.1 with gcc 4.7.2. The numbers look sane by now:

""" chrom start end ref depth r_depth a_depth num_A num_C num_G num_T num_D num_I totQ_A totQ_C totQ_G totQ_T all_ins num_F_A num_F_C num_F_G num_F_T num_F_D num_F_I totQ_F_A totQ_F_C totQ_F_G totQ_F_T all_F_ins num_R_A num_R_C num_R_G num_R_T num_R_D num_R_I totQ_R_A totQ_R_C totQ_R_G totQ_R_T all_R_ins sample_1 1|F0008AAR.2 0 1 C 29 29 0 0 29 0 0 0 0 0 751 0 0 . 0 7 0 0 0 0 0 195 0 0 . 0 22 0 0 0 0 0 556 0 0 . 0|0|0|0,7|195|22|556,0|0|0|0,0|0|0|0,0|.0|.,.|. 1|F0008AAR.2 1 2 T 37 36 1 1 0 0 36 0 0 2 0 0 854 .
"""

Hope it helps,

Darek Kedra