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Old 07-11-2011, 12:08 PM   #1
Hkins552
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Location: Baltimore MD

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Post samtools view error after reheader

I am currently having an issue with samtools view for conversion of .sam to .bam. After replacing the header of my .sam in order to match the ref contigs I think attempted the conversion and received the following output:

$ samtools view -bS 1112-1.reheader.sam > 1112-1.reheader.bam

[sam_read1] reference 'chr1' is recognized as '*'.
[sam_read1] reference 'chr1' is recognized as '*'.
[sam_read1] reference 'chr1' is recognized as '*'.
etc.

Basically for an endless number of lines.

Has anyone seen a similar error?
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Old 07-12-2011, 02:52 AM   #2
pasta
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Maybe this can help: http://seqanswers.com/forums/showthread.php?t=4719
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Old 07-16-2011, 08:13 PM   #3
jjpurwar
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Hi - I received the same error. I also reheadered my sam file and then tried to convert to a bam and received the [sam_read1] reference 'chrX' is recognized as '*'.

Did you ever figure out a solution to the problem?

I noticed that samtools did write a bam file. So, I visualized it (after sorting and indexing it) and it appears that the rest of the chromosomes did convert except for the chrX. I have no reads there. Not surprising.
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Old 07-17-2011, 11:32 AM   #4
jjpurwar
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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.
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