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Search: Posts Made By: Hkins552
Forum: Bioinformatics 12-05-2011, 11:29 AM
Replies: 1
Views: 2,933
Posted By Hkins552
Post 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...
Forum: Bioinformatics 09-14-2011, 11:21 AM
Replies: 3
Views: 5,066
Posted By Hkins552
.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...
Forum: Bioinformatics 08-24-2011, 10:29 AM
Replies: 1
Views: 1,477
Posted By Hkins552
Question 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!
Forum: Bioinformatics 08-22-2011, 11:45 AM
Replies: 1
Views: 2,498
Posted By Hkins552
Post 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...
Forum: Bioinformatics 08-18-2011, 11:02 AM
Replies: 1
Views: 1,624
Posted By Hkins552
Question 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...
Forum: Bioinformatics 08-04-2011, 10:24 AM
Replies: 8
Views: 3,695
Posted By Hkins552
Have you resolved this problem?

Have you resolved this problem?
Forum: Bioinformatics 07-21-2011, 10:35 AM
Replies: 7
Views: 3,436
Posted By Hkins552
$ 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...
Forum: Bioinformatics 07-21-2011, 10:15 AM
Replies: 7
Views: 3,436
Posted By Hkins552
Post Samtools mpileup creates extra large file after local realignment

Hi All,
Typically when running mpileup, my variants.raw.vcf files run around 4-6G (whole exome resequencing). I recently began using local realignment and recalibration of quality score with GATK...
Forum: Bioinformatics 07-13-2011, 09:07 AM
Replies: 17
Views: 6,419
Posted By Hkins552
Is there anyway to avoid using the -I option? I...

Is there anyway to avoid using the -I option? I would still like to call the INDELs on my file. My error is:

[bcf_sync] incorrect number of fields (6 != 5) at 0:33736084
[afs] 0:27544.812...
Forum: Bioinformatics 07-11-2011, 11:08 AM
Replies: 3
Views: 5,052
Posted By Hkins552
Post 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...
Forum: Bioinformatics 07-08-2011, 05:57 AM
Replies: 12
Views: 7,733
Posted By Hkins552
Question 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>...
Forum: Bioinformatics 07-05-2011, 07:16 AM
Replies: 0
Views: 2,117
Posted By Hkins552
Post GATK count covariates error - contig lengths

Hi All,
I have GATK error when inputing the following:

$ java -jar GenomeAnalysisTK.jar -I /input.bam -R /hg19.fasta
-B:dbSNP,VCF /dbsnp.b37.vcf
-T CountCovariates -cov...
Forum: Bioinformatics 07-01-2011, 04:59 AM
Replies: 1
Views: 2,334
Posted By Hkins552
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.
Forum: Bioinformatics 06-28-2011, 09:28 AM
Replies: 1
Views: 1,494
Posted By Hkins552
Post VAAST testing

Is anyone beta-testing VAAST from the Yandell lab? If so, is it looking promising?

Thanks!
Forum: Bioinformatics 06-27-2011, 06:20 AM
Replies: 1
Views: 2,334
Posted By Hkins552
Question GATK RealignerTargetCreator Error = Contigs do not match

I'm trying to do a local realignment using GATK and seem to be stuck at the first step. I've created my ref.dict file and then tried the following script:

$ java -jar gatk -T...
Forum: Bioinformatics 06-15-2011, 10:59 AM
Replies: 8
Views: 5,019
Posted By Hkins552
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?
Forum: Introductions 06-15-2011, 10:37 AM
Replies: 1
Views: 1,435
Posted By Hkins552
Red face 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...
Forum: Bioinformatics 06-15-2011, 09:51 AM
Replies: 2
Views: 6,987
Posted By Hkins552
Question 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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