User: GK1610

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GK161040
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United States
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23 hours ago
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2 years, 3 months ago
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Posts by GK1610

<prev • 44 results • page 1 of 5 • next >
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bamtools stats output
... I have merged 200 bam files using bamtools. When I use bamtools stats options on the merged bam file, I get 117% each for forward strands and reverser strands. why would that happen? it should be 50% for both strands. ********************************************** Stats for BAM file(s): ...
alignment sequencing written 7 days ago by GK161040
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change the columns of vcf file
... I have a genotype hg19_vcf file of 100 individuals with hg19 coordinates. I pull out chromosome, position and rsids from vcf file and use NCBI remap service to convert the coordinates of vcf file to hg38. How do I combine the new coordinates with genotypes information from hg19_vcf file? ...
snp written 15 days ago by GK161040 • updated 5 days ago by Biostar ♦♦ 20
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liftover not giving same number of columns
... I have a WGS file of 200 individuals. The file was aligned using hg19. I want to run liftover to change the coordinates to hg38 I am using vcf-liftover from here https://github.com/wtsi-team144/VCF-liftover cat $my_wgs_vcf_file | vcf-liftover hg19ToHg38.over.chain.gz > output.vcf the outpu ...
genome snp written 6 weeks ago by GK161040
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Comment: C: Liftover error from picard
... I am getting this error now INFO 2018-07-06 11:52:13 LiftoverVcf Loading up the target reference genome. INFO 2018-07-06 11:52:59 LiftoverVcf Lifting variants over and sorting. WARNING 2018-07-06 11:53:06 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target referenc ...
written 3 months ago by GK161040
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Liftover error from picard
... I am trying to align sample genotypes from hg19 to hg38. To do so, I am using liftover from picard on my_vcf_genotype_file (VCF file) chainfile=hg19ToHg38.over.chain.gz java -jar picard-tools-2.5.0/picard.jar LiftoverVcf I=$my_vcf_genotype_file O=$my_vcf_genotype_file.hg38.vcf.gz C=$chain_ ...
software error snp written 3 months 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 3 months ago by GK161040 • updated 3 months ago by Devon Ryan85k
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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 3 months ago by GK161040 • updated 3 months ago by Pierre Lindenbaum113k
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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 4 months 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 5 months ago by GK161040
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Comment: C: verifybamid results with freemix < 2% and chipmix > 10%
... Thanks, this is helpful. ...
written 5 months ago by GK161040

Latest awards to GK1610

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