Question: sam to bam conversion
0
gravatar for sukesh1411
20 months ago by
sukesh141130
South Africa
sukesh141130 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 • 840 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by sukesh141130
1

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

ADD REPLYlink written 20 months ago by WouterDeCoster27k
1

Try -f 4.

ADD REPLYlink written 20 months ago by Devon Ryan78k
1

You should concat the sam file you generated to the header

ADD REPLYlink written 20 months ago by Asaf4.8k
4
gravatar for Carlo Yague
20 months ago by
Carlo Yague3.9k
Belgium
Carlo Yague3.9k 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 COMMENTlink modified 20 months ago • written 20 months ago by Carlo Yague3.9k
0
gravatar for Charles Plessy
20 months ago by
Charles Plessy2.4k
Japan
Charles Plessy2.4k 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 COMMENTlink modified 20 months ago • written 20 months ago by Charles Plessy2.4k
0
gravatar for sukesh1411
20 months ago by
sukesh141130
South Africa
sukesh141130 wrote:

Thank you all of you.. It worked fine.

ADD COMMENTlink written 20 months ago by sukesh141130
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