User: GK1610

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GK161040
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United States
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1 week, 5 days ago
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2 years, 1 month ago
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k****************@gmail.com

Posts by GK1610

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Liftover error from picard
... I am getting this error now INFO 2018-07-06 11:52:13 LiftoverVcf Loading up the target reference genome. INFO 2018-07-06 11:52:59 LiftoverVcf Lifting variants over and sorting. WARNING 2018-07-06 11:53:06 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target referenc ...
written 6 weeks ago by GK161040
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Liftover error from picard
... I am trying to align sample genotypes from hg19 to hg38. To do so, I am using liftover from picard on my_vcf_genotype_file (VCF file) chainfile=hg19ToHg38.over.chain.gz java -jar picard-tools-2.5.0/picard.jar LiftoverVcf I=$my_vcf_genotype_file O=$my_vcf_genotype_file.hg38.vcf.gz C=$chain_ ...
software error snp written 6 weeks ago by GK161040
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Trimming reads of Chipseq samples
... I am using trimmomatic to trim out the adaptor sequences from chip-seq fastq files. I tried Adaptor 1 (TruSeq3-PE-2.fa) file which is default in trimmomatic software and I get 95.77% of both survived reads whereas when I use the adaptor file (A2 see below) with overrepresented sequences I get 80.45% ...
alignment chip-seq written 8 weeks ago by GK161040 • updated 8 weeks ago by Devon Ryan82k
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GATK UnifiedGenotyper doesn't output the variants in vcf files
... Hi I am trying to generate genotype likelihoods from a bam file using UnifiedGenotyper. I am following Pasaniuc Nature genetics 2012 Supplementary note 10 pipeline. The input was java -Xmx4g -jar gatk/3.6-0/src/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ucsc.hg19.fasta -I my.bam -o ...
snp written 8 weeks ago by GK161040 • updated 8 weeks ago by Pierre Lindenbaum111k
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Answer: A: How to filter Michigan genotype imputation results
... try this file=dosage.vcf.gz bcftools view -i 'R2>.8' -Oz $file > $file.filtered.vcf.gz; tabix -p vcf $file.filtered.vcf.gz; ...
written 11 weeks ago by GK161040
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Comment: C: Add AF from 1000 genomes vcf file to a different vcf file
... Thanks. I got this working. Now I am having trouble with editing the vcf file. which means bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/EUR_AF my_vcf > EUR_AF.vcf Now I want to replace EUR_AF with AF and also edit this in the header of the file. ...
written 3 months ago by GK161040
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Comment: C: verifybamid results with freemix < 2% and chipmix > 10%
... Thanks, this is helpful. ...
written 3 months ago by GK161040
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verifybamid results with freemix < 2% and chipmix > 10%
... I ran verifyBAMID on each 200 chip-seq BAM files with input merged vcf file of Genotypes of 600 samples ( 200 of them are chip-seq individuals). I had AF,AC,AN in the info column which was calculated using these genotypes. ~80% of 200 samples are Caucasians. I am struggling to decide for the sampl ...
chip-seq snp sequencing written 3 months ago by GK161040 • updated 3 months ago by WouterDeCoster31k
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Comment: C: Add AF from 1000 genomes vcf file to a different vcf file
... Thanks. its working. ...
written 3 months ago by GK161040
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Add AF from 1000 genomes vcf file to a different vcf file
... I have a **my_vcf** file containing genotypes of 600 individuals. These individuals are from European descent. I want to use AF from 1000 genomes phase 3 project of European population. I have subsetted 100 genomes phase3 vcf file for European population using following command. vcf-subset -c EUR ...
snp written 3 months ago by GK161040 • updated 3 months ago by trausch1.0k

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