Samtools Adding Head reduces file size
Hi all,
I'm trying to convert my SAM to BAM files using samtools, to subsequently view them in IGV. When I do
samtools faidx reference.fasta
samtools view -bt reference.fasta.fai file1.sam > file1.bam
I get the error
[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 1
However, when I'm trying to add the header using the following code, my bam file size reduces massively (from 127mb to 27mb).
samtools view -bt reference.fasta.fai file1.sam > file1.bam
What's going on here and can someone give me a hint on what to do?
Many thanks guys!
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martijnkelder •
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You mean a 127Mb SAM to a 27Mb BAM? BAM is a gzipped (compressed) SAM file. More or less.
IF I dont add '-bt reference.fasta.fai' my BAM file becomes 127mb (similar to SAM), whereas it becomes 27mb when adding that option.
You need the -b option to output a BAM file - hence when you have -b you are getting a compressed binary file of only 27MB.
When you do not have the -b option you are basically outputting in the SAM standard text format, which is uncompressed and gives you the 127MB.
This will correctly give you a SAM to BAM conversion
This will create a file called file1.bam but will be in SAM format not BAM format (just because you call a file .bam doesn't make it a BAM file)