On Mon, 16 Apr 2018, RITSUKO OIKAWA wrote:
Samtools does have an option to *filter* the reads according to regions
specified in the BED format.
$ samtools view -hL chr22_21804028_ref.Gene.bed PLCPRF5bis44.sam >
PLCPRF5bis44.filtered.sam
[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 2
[main_samview] truncated file.
But as above
I get an error message.
Is the command incorrect ?
or
Is sam format different?
We look forward to your reply.
It looks like your input sam file doesn't have any `@SQ` lines to describe
the reference sequences that you're using. They should be at the start of
the file, before any alignment records. What did you use to make the sam
file?
If you have a fasta file with your reference sequences in it, you can use
`samtools dict` to make suitable `@SQ` records. You can prepend the
resulting headers to your original file with a bit of shell scripting. For
example this should add in the @SQ lines while preserving any other
header records that you already have:
head -n 1 PLCPRF5bis44.sam | grep '^@HD' > new.sam
samtools dict -H ref.fa >> new.sam
grep -Ev '^@(HD|SQ)' PLCPRF5bis44.sam >> new.sam
Rob Davies r...@sanger.ac.uk
The Sanger Institutehttp://www.sanger.ac.uk/
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