samtools view without header

Gen2007 · 02-23-2011, 03:03 PM

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 · 02-24-2011, 12:49 AM

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

Gen2007 · 02-24-2011, 09:02 AM

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 · 03-21-2011, 02:45 AM

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

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

Thomas

tanakky · 11-16-2011, 10:58 AM

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

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02-23-2011, 03:03 PM	#1
Gen2007 Member Location: St. Louis Join Date: Jun 2010 Posts: 10	samtools view without header 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!

02-24-2011, 09:02 AM	#3
Gen2007 Member Location: St. Louis Join Date: Jun 2010 Posts: 10	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! Last edited by Gen2007; 02-24-2011 at 09:16 AM.

02-24-2011, 12:49 AM	#2
asangqi Junior Member Location: usa Join Date: Feb 2011 Posts: 4	you can use samtools view -S xx.sam -t chr.list -q 1 > xx.bam.

03-21-2011, 02:45 AM	#4
tmanke Member Location: Germany Join Date: Oct 2009 Posts: 24	Perhaps there is a problem with trailing tabs? I solved a similar problem using sed 's/[ \t]*$//g' samfile Thomas

11-16-2011, 10:58 AM	#5
tanakky Junior Member Location: USA Join Date: Nov 2011 Posts: 1	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