Separate bam file

[m_elena_bioinfo]

Hi NGS users,
anyone knows how I can separate a BAM file in different chromosome?

Starting BAM file is too large (about 10GB for a whole exome) so I want to divide it in different smaller BAM file for chromosome. But using:

> samtools view *sorted.bam | awk '$3=="chr1"' > onlychr1.bam.sorted.bam

returns me an incorrect file.
Infact, when I run
> samtools index onlychr1.bam.sorted.bam

it returns me
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault

Thanx
ME

[quinlana]

You are trying to index a SAM file. You need to change your command to create BAM as follows. Note that you need headers as well.

samtools view -h *sorted.bam | awk '$3=="chr1" || /^@/' | samtools view -Sb -> onlychr1.bam.sorted.bam

Aaron

[m_elena_bioinfo]

It's perfect!
Thank you very much Aaron!!

[m_elena_bioinfo]

A problem!
I aligned my reads vs hg19.fasta (including sequence like chr9_gl000201_random, chrUn_gl000235....).
If I want to split bwa in smaller files (with alignment in two or more chromosome), using Aaron advise:

> samtools view -h *sorted.bam | awk '$3=="chr1" && $3=="chr3" || /^@/' | samtools view -Sb -> onlychr1_3.bam.sorted.bam

the program returns me this error:
[sam_read1] reference 'SN:chr18_gl000207_random LN:4262 ' is recognized as '*'. [main_samview] truncated file.


If I split in single chromosome (only with $3=="chr1"), I have no problem.

Someone can help me?

Thanxxx!!!
ME

[westerman]

I am not an 'awk' expert but I suspect that searching for both $3 being chr1 and $3 being chr3 will indeed give a truncated file -- perhaps not zero length but I suspect that it would not contain much useful information.

E.g., the

'$3=="chr1" && $3=="chr3"

Looks bad to me. I would put parenthesis around the parts to group together.

But caution is due to my non-awk experience.

[m_elena_bioinfo]

You're right westerman, I'm a beginner with awk. But I can't find a system to define the search for both (or more) chromosomes in bam file...

[quinlana]

To find chr1 or chr3 do the following

samtools view -h *sorted.bam | awk '$3=="chr1" || $3=="chr3" || /^@/' | samtools view -Sb -> onlychr1_3.bam.sorted.bam

To find chr1 or chr3 or chr21 do the following

samtools view -h *sorted.bam | awk '$3=="chr1" || $3=="chr3" || $3=="chr21" ||  /^@/' | samtools view -Sb -> onlychr1_3_21.bam.sorted.bam

[us13]

You are trying to index a SAM file. You need to change your command to create BAM as follows. Note that you need headers as well.

samtools view -h *sorted.bam | awk '$3=="chr1" || /^@/' | samtools view -Sb -> onlychr1.bam.sorted.bam

Aaron

I am new to this field but the following worked for me (please let me know if I am wrong):
samtools sort file.bam file.sorted.bam
samtools index file.sorted.bam
samtools view -bh file.sorted.bam chr1 > chr1.file.bam