Error In Sam To Bam Conversion
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9.6 years ago
SK ▴ 110

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?

samtools rnaseq bioinformatics perl bioperl next-gen • 8.8k views
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Could you post line 25645 of your SAM file? And the version number of your samtools?

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Also, what program generated that SAM file?

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9.6 years ago
Rohit ★ 1.5k

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

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9.6 years ago

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.

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

Cheers...

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9.6 years ago
Rohit ★ 1.5k

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.

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9.6 years ago
SK ▴ 110

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

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