[Michael.James.Clark]

This morning Dongliang Ge demonstrated his SequenceVariantAnalyzer at our institute. Sounds promising. It has very nice viewing functionality, but uses lots of memory.

I am not the person doing these analyses. People here use PolyPhen, SeattleSeq, Sift, I don't know what else.

We have used it and I liked it, but unfortunately when we tried it a couple months back, it only took hg18 and annotated SNPs using dbSNP127, which is a little outdated by now. Still a very nice program, though.

[Bruins]

What tools do people use for coding consequence determination after all of this?

This morning Dongliang Ge demonstrated his SequenceVariantAnalyzer at our institute. Sounds promising. It has very nice viewing functionality, but uses lots of memory.

I am not the person doing these analyses. People here use PolyPhen, SeattleSeq, Sift, I don't know what else.

[epigen]

usage of samtools calmd for calculating BAQ

Here.

I just did what was recommended "here" and got the SVN version of samtools that should contain the calmd that calculates BAQ. But now I'm very confused about the parameters when I call this new samtools_svn_816 calmd [Version: 0.1.9-10 (r816)]:

Usage: samtools fillmd [-eubrS] <aln.bam> <ref.fasta>

Options: -e change identical bases to '='
-u uncompressed BAM output (for piping)
-b compressed BAM output
-S the input is SAM with header
-r read-independent local realignment

i.e. the same as in Version 0.1.9 (r783)

Acoording to the manual, there is a difference (highlighted in red):

calmd samtools calmd [-eubSr] [-C capQcoef] <aln.bam> <ref.fasta>

OPTIONS:
-e Convert a the read base to = if it is identical to the aligned reference base. Indel caller does not support the = bases at the moment.
-u Output uncompressed BAM
-b Output compressed BAM
-S The input is SAM with header lines
-C" INT" Coefficient to cap mapping quality of poorly mapped reads. See the pileup command for details. [0]
-r Perform probabilistic realignment to compute BAQ, which will be used to cap base quality.

Can anyone enlighten me whether just the usage message is not up to date or whether there is another version in the SVN?

Thank you in advance

Barbara

[Michael.James.Clark]

Here.

Woosh, thanks. For some reason I was thinking there was more to it (probably because I've been doing half a dozen different approaches each with ten times as many parameters than the BAQ step).

[drio]

Hi Heng,
What do you mean by "cap base quality"?

Can you give more detailed suggestions about how to effectively use BAQ?

We would like to include it in our pipeline but are unsure about how best to utilize it.
Thanks.

Here.

[Michael.James.Clark]

Hi Heng,

3. Cap base quality BAQ (with samtools).

What do you mean by "cap base quality"?

Can you give more detailed suggestions about how to effectively use BAQ?

We would like to include it in our pipeline but are unsure about how best to utilize it.

Thanks.

[lh3]

Does Dindel also do anchor-split mapping, as Pindel? Or the indels discovered by Dindel has to be supported by at least one mappable reads by the aligners, such as bwa/novoalign?

You'd better run Pindel first and then Dindel.

[krobison]

GAMES (according to the paper) uses MySQL queries to go against UCSC; presumably you could easily reroute that to your own data.

A quick look at ANNOVAR suggests it is all flat file based; create your own flat files in the right format and it should work.

[qqcandy]

Does Dindel also do anchor-split mapping, as Pindel? Or the indels discovered by Dindel has to be supported by at least one mappable reads by the aligners, such as bwa/novoalign?

[Balat]

Hi,
Most of the tools related to variant annotations seem to be related to analysing human data. I work on a plant species where we only have the draft genome and not annotated yet. I have done an rna-seq experiment and I have found several snps using samtools. I got a gtf file by aligning reads against the genome sequence with bowtie and tophat. The gtf file only has transcirpt information and no orf or CDS information. Does any one have a script which takes the positions of the snps, annotations from a gtf file and the genome sequence in fasta format and predict if the snps are synonymous or non-synonymous?

[rbagnall]

and ANNOVAR

http://www.openbioinformatics.org/annovar/

and SeattleSeq Annotation

http://gvs.gs.washington.edu/SeattleSeqAnnotation131/

both for annotation of SNP variants. ie. Nonsense, synonymous, splice, intronic, found in 1000 genomes, or HapMap frequency, which gene, amino acid change (from and too, with position) etc.

[krobison]

A new tool, GAMES, just published.

[Michael.James.Clark]

Great, thanks.

There's also SIFT from JCVI ( http://sift.jcvi.org/ ) and PolyPhen ( http://genetics.bwh.harvard.edu/pph/ ). Both very good tools but with some limitations.

[svl]

for coding consequence determination

If you mean how to get the consequence of a variation (whether it's a SNV or a small INDEL) -> we use the ensembl snp effect predictor:

http://www.ensembl.org/tools.html

When using the ensembl perl API you can use this predictor by creating a variation object and get the consequence, which could be any of the ones listed here:

http://www.ensembl.org/info/docs/variation/index.html

/svl

[Michael.James.Clark]

What tools do people use for coding consequence determination after all of this?