Trouble converting SAM to BAM, all 'chrM' recognized as '*'?

SEQanswer · 06-21-2011, 02:01 PM

Hello
I'm trying to convert GERALD output, export.txt files, to BAM.
I used samtools export2sam.pl to convert export.txt to SAM but when using samtools -bt to convert SAM to BAM, all the chrM are being recognized as '*'.
such as
[sam_read1] reference 'chrM' is recognized as '*'.

Can anyone help on why are chrM's causing issues here?

Thanks in advance
Jay

ECO · 06-21-2011, 02:32 PM

Hey Jay,

Let me know what new username you'd like (via PM, or email admin@), as that one ain't gonna work.

Thanks,
-=Eric

SEQanswer · 06-22-2011, 11:34 AM

Issue solved, thanks for help SEQanswers.

ECO · 06-22-2011, 01:21 PM

Jay...posting your solution is helpful too...it may help others in the future.

jjpurwar · 07-16-2011, 08:14 PM

How did you resolve this issue? Please help!

jjpurwar · 07-17-2011, 11:34 AM

I figured out the solution to my problem. Turns out that my sam file header had to be in the right format:

The first line needs to be header.
The second line needs to be a dummy read group line
The next lines need to contain the chromosomes and their lengths.

An example of a good header is as follows:

@HD VN:1.0 SO:unsorted
@RG ID:unknownReadGroup SM:unknownSample
@SQ SN:chrI AS:ce6_32r_index LN:15072421
@SQ SN:chrII AS:ce6_32r_index LN:15279323
@SQ SN:chrIII AS:ce6_32r_index LN:13783681
@SQ SN:chrIV AS:ce6_32r_index LN:17493785
@SQ SN:chrM AS:ce6_32r_index LN:13794
@SQ SN:chrV AS:ce6_32r_index LN:20919568
@SQ SN:chrX AS:ce6_32r_index LN:17718854

Once I deleted all the @SQ , @PG, @HD lines from my sam file and appended the above header text file to my sam file and tried to convert it to a bam - it worked beautifully.

jdilts · 09-16-2013, 10:31 AM

What was wrong with the original header?

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06-21-2011, 02:01 PM	#1
SEQanswer Junior Member Location: MD Join Date: Jun 2011 Posts: 2	*Trouble converting SAM to BAM, all 'chrM' recognized as ''?** Hello I'm trying to convert GERALD output, export.txt files, to BAM. I used samtools export2sam.pl to convert export.txt to SAM but when using samtools -bt to convert SAM to BAM, all the chrM are being recognized as ''. such as [sam_read1] reference 'chrM' is recognized as ''. Can anyone help on why are chrM's causing issues here? Thanks in advance Jay

09-16-2013, 10:31 AM	#7
jdilts Member Location: Richmond, VA Join Date: May 2012 Posts: 10	What was wrong with the original header? What was wrong with the original header?

06-21-2011, 02:32 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Hey Jay, Let me know what new username you'd like (via PM, or email admin@), as that one ain't gonna work. Thanks, -=Eric

06-22-2011, 11:34 AM	#3
SEQanswer Junior Member Location: MD Join Date: Jun 2011 Posts: 2	Issue solved, thanks for help SEQanswers.

06-22-2011, 01:21 PM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Jay...posting your solution is helpful too...it may help others in the future.

07-16-2011, 08:14 PM	#5
jjpurwar Junior Member Location: Salt Lake City Join Date: Jun 2011 Posts: 9	How did you resolve this issue? Please help!

07-17-2011, 11:34 AM	#6
jjpurwar Junior Member Location: Salt Lake City Join Date: Jun 2011 Posts: 9	I figured out the solution to my problem. Turns out that my sam file header had to be in the right format: The first line needs to be header. The second line needs to be a dummy read group line The next lines need to contain the chromosomes and their lengths. An example of a good header is as follows: @HD VN:1.0 SO:unsorted @RG ID:unknownReadGroup SM:unknownSample @SQ SN:chrI AS:ce6_32r_index LN:15072421 @SQ SN:chrII AS:ce6_32r_index LN:15279323 @SQ SN:chrIII AS:ce6_32r_index LN:13783681 @SQ SN:chrIV AS:ce6_32r_index LN:17493785 @SQ SN:chrM AS:ce6_32r_index LN:13794 @SQ SN:chrV AS:ce6_32r_index LN:20919568 @SQ SN:chrX AS:ce6_32r_index LN:17718854 Once I deleted all the @SQ , @PG, @HD lines from my sam file and appended the above header text file to my sam file and tried to convert it to a bam - it worked beautifully.