Forum: Bioinformatics
12-05-2011, 12:29 PM
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Replies: 1
Views: 2,987
Removing Duplicates Scenario Exome Resequencing
I am rethinking my well-established pipeline and trying to tweek it a bit and came across some controversy on the use of remove duplicates. I would like to propose an example scenario and my current...
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Forum: Bioinformatics
09-14-2011, 12:21 PM
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Replies: 3
Views: 5,213
.BED file for Illumina TruSeq Exome
Hi,
I'm looking for a .BED exome feature file to use with bedtools for calculating coverage on my sequencing data which was done on TruSeq Exome Enrichment Kit by Illumina. It's probably obvious...
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Forum: Bioinformatics
08-24-2011, 11:29 AM
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Replies: 1
Views: 1,510
Good Indel Calling Options?
Hi All,
I've found some dated posts regarding indel calling options in GATK, samtools, dindel, etc. What are the most current and suggested pipelines for indel calling?
Thanks!
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Forum: Bioinformatics
08-22-2011, 12:45 PM
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Replies: 1
Views: 2,523
samtools varFilter options
Can anyone explain the exact parsing of varFilter options -d, -D, -G, and -Q during the varFilter step of pileup in samtools? The documentation is a bit hazy...
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Forum: Bioinformatics
08-18-2011, 12:02 PM
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Replies: 1
Views: 1,657
Phasing SNPs from sibs with no parents
Hi All,
I've recently called some SNPs from exome sequencing data on a family consisting of all siblings (no parent data available). I was wondering if there were any programs recommended by the...
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Forum: Bioinformatics
08-04-2011, 11:24 AM
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Replies: 8
Views: 3,786
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Forum: Bioinformatics
07-21-2011, 11:35 AM
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Replies: 7
Views: 3,496
$ samtools mpileup -uf /hg19.fasta...
$ samtools mpileup -uf /hg19.fasta input.sorted.rmdup.reordered.realigned.recalibrated.bam > input.variants.raw
I would like to call just variants, not all loci.
I do not pipe directly to...
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Forum: Bioinformatics
07-21-2011, 11:15 AM
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Replies: 7
Views: 3,496
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Forum: Bioinformatics
07-13-2011, 10:07 AM
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Replies: 17
Views: 6,513
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Forum: Bioinformatics
07-11-2011, 12:08 PM
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Replies: 3
Views: 5,099
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...
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Forum: Bioinformatics
07-08-2011, 06:57 AM
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Replies: 12
Views: 7,893
samtools mpileup floating point error
Hi All,
I am having trouble with mpileup today on samtools.
$ samtools mpileup -uf human_g1k_v37.fasta input.recal.bam > input.variants.raw
[mpileup] 1 samples in 1 input files
<mpileup>...
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Forum: Bioinformatics
07-05-2011, 08:16 AM
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Replies: 0
Views: 2,156
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Forum: Bioinformatics
07-01-2011, 05:59 AM
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Replies: 1
Views: 2,386
Contigs Do Not Match
Still running into the same error. Any input would be greatly appreciated :) In the mean time, I will likely write a script to rename the contigs in the file and see if that pans out.
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Forum: Bioinformatics
06-28-2011, 10:28 AM
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Replies: 1
Views: 1,533
VAAST testing
Is anyone beta-testing VAAST from the Yandell lab? If so, is it looking promising?
Thanks!
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Forum: Bioinformatics
06-27-2011, 07:20 AM
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Replies: 1
Views: 2,386
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Forum: Bioinformatics
06-15-2011, 11:59 AM
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Replies: 8
Views: 5,103
Same problem
I am having the same problem, which is strange as I've used this exact pipeline/command previously with no issues. Have you figured anything out?
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Forum: Introductions
06-15-2011, 11:37 AM
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Replies: 1
Views: 1,482
Hello seq community!
Hello All,
I'm a first year graduate student at Hopkins beggining a new project for our lab involving exome sequencing and analysis en masse. I've been reading your posts for a few months to get...
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Forum: Bioinformatics
06-15-2011, 10:51 AM
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Replies: 2
Views: 7,047
Samtools pipeline produces many indels
Hi All,
I'm new to the community and just beginning to understand many of the programs used for SNP selection. In my current exome seq project, I am looking for homozygous SNPs in a...
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