[lh3]

http://samtools.sourceforge.net/pipe.shtml

[xiang]

Partial pileup for samtools?

samtools pileup takes ages, so does varfilter.

Can samtools pileup work on one chromosome? It would be
must easier for parallelization.

[zlu]

if you use BOWTIE as an alignment algorithm, there is an option (--un) to dump all unmapped reads into a file.

But I'm using BWA. Is there an unmapped flag in the sam file?

[bekkari]

if you use BOWTIE as an alignment algorithm, there is an option (--un) to dump all unmapped reads into a file.

[apfejes]

bekkari:

I believe ConvertToBed.jar in the Vancouver Short Read Analysis Package can do it.

Anthony

[zlu]

Is there a way to convert a SAM consensus output (using -c option for pileup) to the old maq-style .cns consensus?

I have some maq-based pipelines I would like to use on my BWA results.

Has anyone had any luck with this? In addition, in MAQ, you can dump unmapped reads into a separate file, is there such a function/tool in samtools? Thank you.

[bekkari]

Does any one know about any tool/program to convert SAM output to BED format, if so please let me know

[jnfass]

samtools pileup for multiple diploid individuals?

Is it appropriate to use samtools pileup (which uses maq's consensus- and SNP-calling model) on pooled reads from multiple diploid individuals? I'm looking for SNPs both within the read population, and between the reads and the reference. I've got 6 individuals in separate samples from a species close to the reference, at low enough depth where I should probably just forget about mapping each individual separately (in other words, I can forget about calling a genotype for each individual). But I'd still like to call the most likely consensus and SNP for this population ...

[seq_GA]

Hi
I amnot able to use picard.
I get the following error.

java picard-1.07.jar -h
Exception in thread "main" java.lang.NoClassDefFoundError: picard-1/07/jar

Thanks.

[jmj1091]

Heng,
Thanks for your help! I checked out the latest revision from the svn repository, and, indeed, the new pileup (as generated with the -a flag) does not have the disagreements.

[lh3]

@jmj1091

This is a known issue and only affects repetitive regions. It is annoying, I admit. In the SVN version of samtools, I implemented a simplified version of SOAPsnp model which does not have this issue.

@bekkari

It is likely that cufflinks is using some optional tags specific to tophat but not available in all SAM files.

[bekkari]

SAM format versions?

Can some one help me understand if there are any versions in SAM format. Cufflinks program works well with SAM format output by TOPHAT program but fails when the SAM output comes from Bowtie or bwa. Did anyone had encountered this before, if so please suggest.

[jmj1091]

Hi,
I have a question about how samtools pileup generates the consensus sequence. I recently ran an alignment that output mappings only when there were no mismatches between the read and the reference. I proceeded to generate the pileup, and noticed that, although there are no mismatches throughout, there are multiple positions where the consensus sequence differs from the reference. tview confirmed that, at these positions, all of the reads mapped agree with the reference, yet the consensus base is different! I did notice that the reads' bases were of low Phred quality at those locations, and I was wondering if perhaps pileup occasionally mutates the consensus base if its quality score is sufficiently low. I tried looking through the source code, but I couldn't figure it out. Is this a bug?
Thanks!

[liu3zhen]

File with the Pileup format was generated by the command below:
samtools pileup -f ref.fas reads.aln.sorted.bam > reads.pileup

Here are partial results:
chr1 7 C 1 ^~. B
chr1 8 A 1 . C
chr1 9 A 1 . C
chr1 10 A 1 . C
chr1 11 G 1 . A
chr1 12 C 1 . B
chr1 13 C 1 . B
chr1 14 A 1 . C
chr1 15 A 1 . C
chr1 16 A 1 . B

But when I ran:
samtools.pl varFilter test -d 3

error was shown as:
Use of uninitialized value in numeric lt (<) at /mnt/01/liu3zhen/analysisTool/SAMtools/samtools-0.1.6_x86_64-linux/samtools.pl line 78.


pileup file only contain 6 columns. In the samtools.pl, at least 8 columns are required for the command of line 78.


My questions are:

1. Is the pileup output correct?
2. Am I understanding corretly about code of line 78?

Thank you very much.

I know what's going on here. I have use -cv for the pileup step to report variations. Thanks.

[liu3zhen]

File with the Pileup format was generated by the command below:
samtools pileup -f ref.fas reads.aln.sorted.bam > reads.pileup

Here are partial results:
chr1 7 C 1 ^~. B
chr1 8 A 1 . C
chr1 9 A 1 . C
chr1 10 A 1 . C
chr1 11 G 1 . A
chr1 12 C 1 . B
chr1 13 C 1 . B
chr1 14 A 1 . C
chr1 15 A 1 . C
chr1 16 A 1 . B

But when I ran:
samtools.pl varFilter test -d 3

error was shown as:
Use of uninitialized value in numeric lt (<) at /mnt/01/liu3zhen/analysisTool/SAMtools/samtools-0.1.6_x86_64-linux/samtools.pl line 78.


pileup file only contain 6 columns. In the samtools.pl, at least 8 columns are required for the command of line 78.


My questions are:

1. Is the pileup output correct?
2. Am I understanding corretly about code of line 78?

Thank you very much.