Count exact match reads in SAM file

Question

[AHW]

I got the alignment result in SAM format using bowtie2. As bowtie2 does not have the setting for exact match, so I want to count the number of exact match.

I tried to use grep to extract the exact reads using grep AS:i:0 old.sam >> newfiltered.sam and when I try to count by samtools using samtools view -c newfiltered.sam, I get the following error

[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 1
[main_samview] truncated file.

I would like to know how can I count the exact matches in the file.

[Sej Modha]

When you use the first grep command on old.sam, you are losing the header information in newfiltered.sam, that's why samtools view command results in the error mentioned above.

See: http://seqanswers.com/forums/showthread.php?t=12849 and http://seqanswers.com/forums/showthread.php?t=58221 for further details about extracting reads.

[AHW]

Thank you for your comment. I tried using BBMap and I used the command reformat.sh in=output.sam out=exact.fastq, however, I am not able to find how to extract exact matching reads. The given command extracts all the reads to the new file.