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

[SEQanswer]

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]

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]

Issue solved, thanks for help SEQanswers.

[ECO]

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

[jjpurwar]

How did you resolve this issue? Please help!

[jjpurwar]

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]

What was wrong with the original header?

What was wrong with the original header?