Error In Sam To Bam Conversion

Question

[SK]

I want to convert SAM file into BAM. I am using command

samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam

but getting error

Parse error at line 25645: invalid CIGAR character

Could someone please help me to solve this problem?

[Christof Winter]

Could you post line 25645 of your SAM file? And the version number of your samtools?

[Rohit]

Could you please try:

samtools view -b -S bowtie.glob.bam bowtie.glob.sam

This is because -b already gives bam output and -S as sam input. This might help.

[SK]

Thanks Rohit, but samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam is the same command that I used.

[fo3c]

Also, what program generated that SAM file?

Answer 1

[Rohit]

I went through it, the solution is to add the index file. Create the index files with

samtools faidx sequence.fa

This creates the index file *.fai. The final command for conversion is

samtools view -bt sequence.fa.fai -S bowtie.glob.sam -o bowtie.glob.sam

Cheers,
Rohit

Answer 2

[Ashutosh Pandey]

I know you have got the solution but here is what is mentioned in the samtools manual:

Import SAM to BAM when @SQ lines are present in the header:

samtools view -bS aln.sam > aln.bam

If @SQ lines are absent:

samtools faidx ref.fa 
samtools view -bt ref.fa.fai aln.sam > aln.bam

where ref.fa.fai is generated automatically by the faidx command.

[Rohit]

The manual was where I got the solution from... Forgot to mention that...

Cheers...