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Old 07-11-2011, 11:08 AM   #1
Location: Baltimore MD

Join Date: Jun 2011
Posts: 18
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 '*'.

Basically for an endless number of lines.

Has anyone seen a similar error?
Hkins552 is offline   Reply With Quote
Old 07-12-2011, 01:52 AM   #2
Location: Alps

Join Date: Jan 2011
Posts: 27

Maybe this can help:
pasta is offline   Reply With Quote
Old 07-16-2011, 07:13 PM   #3
Junior Member
Location: Salt Lake City

Join Date: Jun 2011
Posts: 9

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.
jjpurwar is offline   Reply With Quote
Old 07-17-2011, 10:32 AM   #4
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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.
jjpurwar is offline   Reply With Quote

chr1, conversion, header, recognized, sam

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