sam to bam conversion

Question

[sukesh1411]

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..

[WouterDeCoster]

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

[Devon Ryan]

Try -f 4.

[Asaf]

You should concat the sam file you generated to the header

Answer 1

[Carlo Yague]

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

Answer 2

[Charles Plessy]

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.

Answer 3

[sukesh1411]

Thank you all of you.. It worked fine.