samtools view without header

[Gen2007]

Hi All,

I'm having trouble filtered MAQ aligned reads from a sam file with no header and converting to BAM. I've tried created the fai file of the reference as suggested by the SAMTOOLS faq, but to no avail.

When I use the following command:
samtools view -S lane1.normal.sam -T reduced.reference.fa -q 1

I get an error: "Parse error at line 1: missing colon in auxiliary data"

Does anyone have any suggestions?

Thanks a lot!

[asangqi]

you can use samtools view -S xx.sam -t chr.list -q 1 > xx.bam.

[Gen2007]

i implemented the command you suggested, asanggi:

samtools view -S xx.sam -t reference.fa.fai -q 1 > xx.bam

but i still get the same error.

thanks for your help!

[tmanke]

Perhaps there is a problem with trailing tabs?
I solved a similar problem using

sed 's/[ \t]*$//g' samfile

Thomas

[tanakky]

I had the same problem, but I could solve with two following command

sed 's/[ \t]*$//g' samfile (same with Thomas)
tr -d \\r < samfile > samfile.2

Thanks
Yoshiaki