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Question: sam to bam conversion
0
gravatar for sukesh1411
3.5 years ago by
sukesh1411 • 30
South Africa
sukesh1411 • 30 wrote:

Hi

I could extract the unmapped reads from the bwa-mem alignment file in SAM format using below command

samtools view -S -f0x4 alnIRGSP.sam > UNMAP.sam.

After that i could not convert this sam file to bam file . I get the below error.

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "sortUNMAP.sam".

Can anyone help me to solve this..
samtools • 2.0k views
ADD COMMENT • link •
modified 3.5 years ago • written 3.5 years ago by sukesh1411 • 30
1

This is a question, not a tool. Please use the 'post type' accordingly.

ADD REPLY • link written 3.5 years ago by WouterDeCoster ♦ 42k
1

Try -f 4.

ADD REPLY • link written 3.5 years ago by Devon Ryan ♦ 94k
1

You should concat the sam file you generated to the header

ADD REPLY • link written 3.5 years ago by Asaf ♦ 6.9k
4
gravatar for Carlo Yague
3.5 years ago by
Carlo Yague • 4.9k
Canada
Carlo Yague • 4.9k wrote:

use -h (include header) :

samtools view -h -f 4 -S alnIRGSP.sam > UNMAP.sam

u can also output bam directly with -b:

samtools view -h -b -f 4 -S alnIRGSP.sam > UNMAP.bam
ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Carlo Yague • 4.9k
0
gravatar for Charles Plessy
3.5 years ago by
Charles Plessy • 2.7k
Japan
Charles Plessy • 2.7k wrote:

The error message indicates that the program you use expects data in the BAM (binary) format. However, you are using a SAM (text) file as input. The program reads it as if it were a BAM file, and stops when it detects that it can not find the BAM binary header. Use the -b option of samtools for outputting in BAM format.
ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Charles Plessy • 2.7k
0
gravatar for sukesh1411
3.5 years ago by
sukesh1411 • 30
South Africa
sukesh1411 • 30 wrote:

Thank you all of you.. It worked fine.
ADD COMMENT • link written 3.5 years ago by sukesh1411 • 30
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