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Forum: Bioinformatics 08-17-2012, 12:44 AM
Replies: 2
Views: 1,547
Posted By wanguan2000
hello, when i run the example of crossbow i got...

hello, when i run the example of crossbow i got this problem:

Crossbow expects 'bowtie' to be at path /home/wanguan2000/hadoop_soft/crossbow-1.2.0/bin/bowtie on the workers
Crossbow expects...
Forum: Bioinformatics 05-23-2012, 01:39 AM
Replies: 6
Views: 5,809
Posted By wanguan2000
http://gene-seq.vicp.net/2012/05/mouse-mm9-dbsnp_1...

http://gene-seq.vicp.net/2012/05/mouse-mm9-dbsnp_132-vcf-version/
maybe U can try this daatabase:
We are pleased to announce the release of VCF version dbSNP build 132, available on the mouse...
Forum: Bioinformatics 05-23-2012, 01:38 AM
Replies: 0
Views: 1,908
Posted By wanguan2000
mouse mm9 dbSNP_132 VCF version

We are pleased to announce the release of VCF version dbSNP build 132, available on the mouse assembly (UCSC/mm9). dbSNP build 132 is available at NCBI.

This dbSNP_132 VCF version can be used to...
Forum: Bioinformatics 12-29-2011, 11:24 PM
Replies: 48
Views: 57,164
Posted By wanguan2000
GQ The Genotype Quality calculation

GQ:21.05
PL:221,21,0
you had made a calculation error.

P(D|AA) = 10^(-22.1) = 7.943282e-23
P(D|AG) = 10^(-2.1) = 0.007943282
P(D|GG) = 10^(0) = 1
1 - 1/(1+7.943282e-23+0.007943282) =...
Forum: Bioinformatics 12-27-2011, 05:36 PM
Replies: 2
Views: 4,362
Posted By wanguan2000
vcf-compare Compares positions in two or...

vcf-compare

Compares positions in two or more VCF files and outputs the numbers of positions contained in one but not the other files; two but not the other files, etc, which comes handy when...
Forum: Bioinformatics 12-25-2011, 11:29 PM
Replies: 20
Views: 8,253
Posted By wanguan2000
Which software is better now, I just have very...

Which software is better now, I just have very good data(whole genomes, and exome sequecing) sets can be used to test.
Forum: Bioinformatics 12-12-2011, 07:48 PM
Replies: 1
Views: 2,177
Posted By wanguan2000
VariantAnnotator ReadPositionRankSumTest Error

my command:
java -Xmx20g -jar GenomeAnalysisTK-1.3-24-gc8b1c92/GenomeAnalysisTK.jar \
-T VariantAnnotator \
-R hg19fastadatabase/ucsc.hg19.fasta \
-I dedup_mate_recal.bam \
--variant...
Forum: Genomic Resequencing 11-29-2011, 07:50 PM
Replies: 27
Views: 14,824
Posted By wanguan2000
Thank U for garwuf explanation. I think:You mean...

Thank U for garwuf explanation. I think:You mean samtools 0.1.15 better than GATK for ploidy SNP Calling?
Both samtools and GATK SNP VCF results have heterozygosis SNP for ploidy, and those SNPs are...
Forum: Genomic Resequencing 11-28-2011, 11:20 PM
Replies: 27
Views: 14,824
Posted By wanguan2000
what about samtools vs GATK snp efficiency for...

what about samtools vs GATK snp efficiency for ploidy?
Forum: Bioinformatics 11-24-2011, 09:36 PM
Replies: 1
Views: 1,506
Posted By wanguan2000
SNP calling reads number

I followed the GATK pipeline.
when I use the IGV to see the bam file I found the question:
position chr17:7578524 : G(51 reads)-A(20 reads) I think this is a snp, but the position doesn't exist...
Forum: Bioinformatics 11-24-2011, 09:23 PM
Replies: 0
Views: 2,283
Posted By wanguan2000
GATK snp calling

The number of LowQual using ApplyRecalibration as the same as the LowQual in raw.vcf.
LowQual number does not change!!! and a little PASS change to TruthSensitivityTranche99.00to99.90.
should I...
Forum: Bioinformatics 11-24-2011, 09:20 PM
Replies: 2
Views: 4,306
Posted By wanguan2000
Somatic SNP

about somatic-sniper result.
For an example of Somatic SNP which come from somatic-sniper :
cancer: G(40 reads)-A(16 reads)
normal : G(38 reads)-A(7 reads)
I think this SNP can't be...
Forum: Bioinformatics 11-22-2011, 04:36 AM
Replies: 4
Views: 3,157
Posted By wanguan2000
I have the same question. And I found the number...

I have the same question. And I found the number of LowQual using ApplyRecalibration as the same as the LowQual in raw.vcf.
LowQual number does not change!!! and a little PASS change to...
Forum: Genomic Resequencing 11-13-2011, 05:59 PM
Replies: 27
Views: 14,824
Posted By wanguan2000
I confused the freebayes's commdane: -H...

I confused the freebayes's commdane:
-H --diploid-reference
If using the reference sequence as a sample (default),
treat it as diploid. default: false (reference is haploid)
###########
My...
Forum: Genomic Resequencing 11-13-2011, 07:11 AM
Replies: 27
Views: 14,824
Posted By wanguan2000
I confused the freebayes's commdane: -H...

I confused the freebayes's commdane:
-H --diploid-reference
If using the reference sequence as a sample (default),
treat it as diploid. default: false...
Forum: Bioinformatics 10-26-2011, 05:14 AM
Replies: 15
Views: 31,393
Posted By wanguan2000
XM Number of mismatches in the alignment

XM Number of mismatches in the alignment
Forum: Bioinformatics 10-26-2011, 05:11 AM
Replies: 6
Views: 5,542
Posted By wanguan2000
in bwa: XM Number of mismatches in the...

in bwa:
XM Number of mismatches in the alignment
MD Mismatching positions/bases
Forum: Bioinformatics 10-24-2011, 05:38 AM
Replies: 9
Views: 8,752
Posted By wanguan2000
Today, I have the same problem like U said. I...

Today, I have the same problem like U said.
I have alignment whole genome sequencing pair-end data.(r1.fastq 140G ,r2.fastq 130G)
and centos6 with memory 64G
But when I do BWA sampe, I got the...
Forum: Bioinformatics 09-11-2011, 12:27 AM
Replies: 2
Views: 3,692
Posted By wanguan2000
ps: s1_raw_indel.vcf file contains total of 8454...

ps: s1_raw_indel.vcf file contains total of 8454 indels, are the number is few variants and these annotations is unsafe?
Forum: Bioinformatics 09-10-2011, 09:58 PM
Replies: 2
Views: 3,692
Posted By wanguan2000
problem about GATK indel VQSR

java -Xmx4g -jar GenomeAnalysisTK-1.1-36-g367bbee/GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R ucsc.hg19.fasta \
-B:input,VCF s1_raw_indel.vcf \...
Forum: Bioinformatics 08-03-2011, 06:52 PM
Replies: 0
Views: 3,655
Posted By wanguan2000
GATK VariantFiltration undefined variable AB

java -Xmx4g -jar ./GenomeAnalysisTK-1.1-12-g2d94037/GenomeAnalysisTK.jar \
-l INFO \
-nt 8 \
-R ucsc.hg19.fasta \
-T UnifiedGenotyper \
-I...
Forum: Bioinformatics 07-24-2011, 08:32 PM
Replies: 2
Views: 2,543
Posted By wanguan2000
java -Xmx4g -jar...

java -Xmx4g -jar /share/user_data/wfz1/wangguan/GATK/GenomeAnalysisTK-1.1-3-g1f8fc4a/GenomeAnalysisTK.jar \
-T SomaticIndelDetector \
-l INFO \
-R ./hg19fasta/ucsc.hg19.fasta \
...
Forum: Bioinformatics 07-24-2011, 07:30 PM
Replies: 2
Views: 2,543
Posted By wanguan2000
GATK IndelGenotyperV2 ERROR

when I followed the pipeline:
http://www.broadinstitute.org/gsa/wiki/index.php/Whole_exome_v1

java -Xmx4g -jar GenomeAnalysisTK.jar \
-l INFO \
-nt 8 \
-R ./hg19fasta/ucsc.hg19.fasta \
...
Forum: The Pipeline 11-17-2010, 02:03 AM
Replies: 1
Views: 7,302
Posted By wanguan2000
Help finish the pipeline for human whole exome sequencing with paired reads data

The pipeline for human whole exome sequencing with paired reads data


A, Align samples to genome (BWA): get BAM files
bowtie
1./bowtie -t -y -S hg18 -1 reads_1.fq -2 reads_2.fq reads.sam
...
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