[aby]

I converted the all.map file generated from MAQ tool to SAM format using maq2sam-long in samtools. The output file I named as Out. Now when I try to convert Out file (which is in SAM format) to BAM format using the command
samtools view -S Out

I get an error message that header @ not found. When I edit the Out file by manually adding @ at the top, more errors appear. What should I do? Is there a fault in the SAM file generated by the converter maq2sam ? Is there any other way to convert SAM file to BAM file? I tried 'samtool import' and that also does not work.

[aby]

I was trying to convert my single read illumina file to SAM format using the export2sam.pl script. It does not work and gives the following error:

Use of uninitialized value $t[21] in string ne at export2sam.pl line 67, <$fh1> line 14063.

Here is a sample data from my file.

HWUSI-EAS174_0025:2:1:5:488#0/1:CGGAGAATACGCTCCCATTCCCCCNGNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNTGATCTTAGATCGGA:aabbbbb_baaa_a]ab`_aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
HWUSI-EAS174_0025:2:1:5:1542#0/1:TGGATGCCTAGGCAATCAGAGGCGNANANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANGTGATAAGCAGCGAA:abbbabbbbbbbbbbbbbbbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB


How do I resolve it ? Is there any other way?

A.

[bosTau2]

It depends on regions. If a region is repetitive then you need to filter out possible duplications which can cause artificial hetero SNPs. "Repetitive" here means kmer uniqueness --- how many times a given kmer (30mer for example) can be found in a reference.

[sbaheti]

Hi lh3

Originally Posted by xguo
I got a list of candidate SNPs using BWA and samtools for RNASeq data, and am trying to weigh various filtering options. "samtools.pl varFilter" gives a list of filtering criterion with default setting. The maximum read depth is set at 100. Given that duplicate reads have been removed by "samtools rmdup", do I still need to limit the maximum read depth?

replied by lh3:
Yes, you need this unless you are doing target sequencing in which case the read depth is expected to vary a lot.

My question

If we are doing variant calling in exome capture analysis, do i need to limit the max read depth when using samtool varFilter tool?

[wuhoucdc]

Dear All,

Do you know if samtools can perform multiple commands (>2) together? Here assuming that I have ten BAM files (result001.bam, result002.bam,......result010.bam) and want to merge them first and then sort and index them, the last step I hope is to extract the data for chromosome 1 (chr1), how can I edit the samtools command? I did it like this:
samtools merge result.bam result001.bam result002.bam ............result010.bam |\
samtools sort - result | \
samtools index result.bam | \
samtools view result.bam chr1 > resultchr1.bam

Is it right?

Thank you very much!

Wu

[bosTau2]

Is there sam2maq (sam to maq map format)? I am testing simulated data and like to convert ssaha2 alignment to maq output so that I can analyze them in maq. I cerated all the simu data in maq.
Thank you.

[KevinLam]

There was a discussion on how the CS tag should be generated in sam files according to the specs. Is there a consensus on how it is to be done?

I have to write a script to append the CS tag info to the BWA alignment of SOLID reads. I am hoping to make it as painless as possible.

[KevinLam]

Thanks Li Heng. I just want to confirm that nothing is wrong with the sorted bam file.

Thanks a lot.

You may convert to sam and count the lines as a proxy for checking.
but yes as lh3 mentioned sorted files compress better due to the compression algorithm

[gsjlucky]

maq2sam-long

maq2sam-short is for the .map files generated by maq-0.6.x, while maq2sam-long for files generated by maq-0.7.x. Sorry for the confusion, and one of the aims of SAM is to avoid such confusions in future.

maq2sam <in.map> [<readGroup>], I want know how to use the option parameter 'readGroup',can it add library info from map to sam?

[glacierbird]

@corthay

You can convert with "blast2sam.pl -s" to save the sequence in SAM. Currently, samtools cannot parse SAM without sequence, although the specification allows this.

Hi Li,
I parse .sam with sequence, but samtools view still gave such error msg. Could you please take a look of the post:

http://seqanswers.com/forums/showthread.php?p=21003#post21003

Thanks.

[win804]

You already asked this on a separate thread
http://seqanswers.com/forums/showthread.php?t=5684

Yes, I wanted to delete the previous thread before, however, I have no idea of how to do it. Any idea?

Thanks.

[win804]

Thanks Li Heng. I just want to confirm that nothing is wrong with the sorted bam file.

Thanks a lot.

[maubp]

Hi All,
Is "sorted" BAM file smaller in size compare to unsorted BAM file?
If that's the case, why is that so?...

You already asked this on a separate thread

http://seqanswers.com/forums/showthread.php?t=5684

[lh3]

Sorted files are compressed better.

[win804]

Hi All,
Is "sorted" BAM file smaller in size compare to unsorted BAM file?
If that's the case, why is that so?

I sort a lot of BAM files using the samtools, with this command:
samtools sort chr1-aligned.bam chr1-aligned.sorted

file size of chr1-aligned.bam ==> 353,618,735 bytes
but the file size of chr1-aligned.sorted.bam ==> 295,208,534 bytes

I have checked for all my unsorted and sorted bam files. All of the sorted bam files are smaller in size compare to the unsorted ones.

Thanks.