Hello,
I am looking to use mpileup for base calling. Previously I ran samples together but could not find any sample specific read count/quality...
14 results in 0.0029 seconds.
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mpileup sample specific read count/quality info
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classifying a variant as het or hom
Hi all,
I have a general question. Assume I have a genomic position which had nice sequence coverage and quality at the position (i.e. all metrics... -
Samtools multisample SNP caller
Hi -
I am running a comparison between running samtools SNP calling in the multi sample mode, vs using it on each file individually. I seem...Last edited by amcrisan; 11-06-2013, 03:56 PM. -
SNP Analysis Tools for SOLiD
Hi all,
I've just completed sequencing and aligning data from 200 patients and was wondering if what would be the best SNP calling tools... -
Variant Detection Software Review
Just trying to get a feel for the pros and cons of all the variant detection algorithms that are out there before I choose one algorithm.
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SNPs from populations
Hi,
I'm a cetacean population geneticist in San Diego, CA, and I'm trying to use Illumina resequencing of nuclear loci (from capture-array enriched... -
SNP detection (no reference) parameters
Hello,
I have sequenced the transcriptome of a non-model animal, including RNA from 4 different tissues of 10 individuals and normalizing.... -
Editing assembly output of amos?
Hello Everyone,
I hope for the love of god that someone might be able to point me in the right direction.
Essentially, I... -
Strand SI introduces Avadis NGS. NGS analysis for the rest of us!
Strand Scientific Intelligence is happy to announce the release of Avadis NGS. NGS analysis for the rest of us!
Avadis NGS is an application... -
Non-commercial SNP calling soft
I noticed that information on SNP calling and SNP discovery (especially!) software for NGS is quite scarce
. Are there any good tools available...
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GATK unified SNP caller error
Hi,
Thanks for nice piece of software. I have been trying out the UnifiedGenotyper but am having some issues with it. It crashes if I... -
Snp discovery without a reference
I have paired-end (76bp) output from a GA in which I would like to try snp discovery. The hiccup is there is no reference genome for my specie.
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MAQ: SNPs interpretation, etc!
I'm a graduate student just starting to work with Maq for calling SNPs from Illumina resequencing of the Giardia genome. I'm a bit unsure about appropriate... -
SOAP aligner output format? and composite quality scores?
Hi,
could someone please tell me what the output of SOAP aligner looks like (e.g. one sample line, with explanation of what the various...
