Corrupt BAM file

[ashkot]

Hi all, i have come across a strange problem. I am getting a chromosome SAM file from 1K genomes using the following command, for e.g.

samtools view -h ftp://ftp-trace.ncbi.nih.gov/1000gen...e.20101123.bam 11 > test.sam

(please note its for the entire chromosome 11).

Now I want to convert test.sam into a bam file so i use the following command
samtools view -bS test.sam -o test1.bam

The problem is in test1.bam, when i open it with gedit the first few characters are

BAM\A3>\00\00@HD

and the very end of the file is again full of junk

T\00\00\00\00\00\001\00=C\DB\00\00\002\00\8D\ED~\00\00\003\00\95\CD\00\00\004\00d\C8d\00\00\005\00<\8C\C8
\00\00\006\00;3
\00\00\007\00gC| \00\00\008\00vV\B9\00\00\009\00\F7\BEj\00\00\0010\00\9B\00\00\0011\004 \00\00\0012\00\F7j\FA\00\00\0013\00VZ\DD\00\00\0014\00$f\00\00\0015\00@\81\00\00\0016\00A\B4b\00\00\0017\00\CA\F0\D6\00\00\0018\00@]\A7\00\00\0019\00\97<\86\00\00\0020\00p\B1\C1\00\00\0021\00gg\DE\00\00\0022\00v\D8\00\00\00X\00\A0=A \00\00\00Y\00\FE\F7\89\00\00\00MT\00\B9@\00\00\00\00\00GL000207.1\00\A6\00\00\00\00\00GL000226.1\00\A0:\00\00\00\00\00GL000229.1\00\C9M\00\00\00\00\00GL000231.1\00\FAj\00\00\00\00\00GL000210.1\00"l\00\00\00\00\00GL000239.1\00 \84\00\00\00\00\00GL000235.1\00\AA\86\00\00\00\00\00GL000201.1\004\8D\00\00\00\00\00GL000247.1\00F\8E\00\00\00\00\00GL000245.1\00+\8F\00\00\00\00\00GL000197.1\007\91\00\00\00\00\00GL000203.1\00z\92\00\00\00\00\00GL000246.1\00
\95\00\00\00\00\00GL000249.1\00f\96\00\00\00\00\00GL000196.1\00\98\00\00\00\00\00GL000248.1\00j\9B\00\00\00\00\00GL000244.1\00\F9\9B\00\00\00\00\00GL000238.1\00\9C\00\00\00\00\00GL000202.1\00\A7\9C\00\00\00\00\00GL000234.1\00S\9E\00\00\00\00\00GL000232.1\00̞\00\00\00\00\00GL000206.1\00)\A0\00\00\00\00\00GL000240.1\00ͣ\00\00\00\00\00GL000236.1\00Σ\00\00\00\00\00GL000241.1\00\A8\A4\00\00\00\00\00GL000243.1\00M\A9\00\00\00\00\00GL000242.1\00\AA\00\00\00\00\00GL000230.1\00\AB\AA\00\00\00\00\00GL000237.1\00+\B3\00\00\00\00\00GL000233.1\00u\B3\00\00\00\00\00GL000204.1\00\9E=\00\00\00\00GL000198.1\00\E5_\00\00\00\00GL000208.1\00j\00\00\00\00GL000191.1\00\C1\9F\00\00\00\00GL000227.1\00v\F5\00\00\00\00GL000228.1\00`\F8\00\00\00\00GL000214.1\00\F6\00\00\00\00GL000221.1\00_\00\00\00\00GL000209.1\00\C1m\00\00\00\00GL000218.1\00{u\00\00\00\00GL000220.1\00
x\00\00\00\00GL000213.1\00\8F\81\00\00\00\00GL000211.1\00\A6\8A\00\00\00\00GL000199.1\00\92\97\00\00\00\00GL000217.1\00u\A0\00\00\00\00GL000216.1\00\A1\00\00\00\00GL000215.1\00\A2\00\00\00\00GL000205.1\00\FC\A9\00\00\00\00GL000219.1\00\FE\BB\00\00\00\00GL000224.1\00\ED\BD\00\00\00\00GL000223.1\00\E7\C0\00\00\00\00GL000195.1\00p\CA\00\00\00\00GL000212.1\00\EA\D9\00\00\00\00GL000222.1\00\ED\D9\00\00\00\00GL000200.1\00\9B\DA\00\00\00\00GL000193.1\00]\E5\00\00\00\00GL000194.1\00\ED\EB\00\00\00\00GL000225.1\00\E58\00\00\00\00GL000192.1\00\A8Z\00

Can anyone please tell me why this may be occurring?

Thanks in advance.

Ashwin

[swbarnes2]

Your first command, "samtools view -h" converts a compressed, binary file into an uncompressed human-readable SAM file.

"samtools view -bS" turns that human readable file back into a compressed binary, which is no longer human readable. So it makes sense that it look like garbage, it's not supposed to be text.

I don't think you really mean to be uncompressing the whole chr 1 file locally onto your computer. I think you want to just transfer the .bam file as it is, and use "samtools view" with a chromosome and region if you want to look with your eyes at a subset individual lines. Otherwise, leave it as a bam, unless you are quite sure that your downstream tools can't handle .bam format. Most software; samtools, picard, GATK, etc, work with compressed bam files fine. No one wants to have to uncompress everything into .sam format to work with it, so those programs are designed to work with nice, compressed .bams.

[ashkot]

Thank you

Thanks for the insight, this has sorted my problem.