User: GK1610

gravatar for GK1610
GK161030
Reputation:
30
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New User
Location:
United States
Last seen:
2 days, 9 hours ago
Joined:
1 year, 10 months ago
Email:
k****************@gmail.com

Posts by GK1610

<prev • 36 results • page 1 of 4 • next >
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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 10 days ago by GK161030
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Comment: C: verifybamid results with freemix < 2% and chipmix > 10%
... Thanks, this is helpful. ...
written 10 days ago by GK161030
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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 10 days ago by GK161030 • updated 10 days ago by WouterDeCoster28k
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Comment: C: Add AF from 1000 genomes vcf file to a different vcf file
... Thanks. its working. ...
written 10 days ago by GK161030
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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 11 days ago by GK161030 • updated 10 days ago by trausch1.0k
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What is chipmix and freemix in verifybamid
... have question on FREEMIX parameter I have this from you Hyun Min Kang "The key idea of FREEMIX estimate is to use excessive heterozygosity to estimate the level of contamination. Especially for common SNPs, you will observe higher fraction of heterozygous alleles than 2*p*(1-p), and it turns out t ...
snp sequencing written 15 days ago by GK161030
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Comment: C: bcftools to GATK
... you are right I have like ~240 samples I combined 20 samples first and created 12 meta-merged files for each chromosome and when I remerge these meta-merge files. I get this error of java.lang.IllegalArgumentException: Unexpected base in allele bases '*AAAAAAAAC' https://gatkforums.broadinstitut ...
written 8 weeks ago by GK161030
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Comment: C: bcftools to GATK
... Yes I get that. My problem is I want to remove indels from my gvcf files before I start combinGVCFs to merge GVCF files. I am using this command. java -Xmx2g -jar $GenomeAnalysisTK_jar SelectVariants -R $REF -V $file -O output.vcf.gz --select-type-to-exclude INDEL Unfortunately it does nothing. wh ...
written 8 weeks ago by GK161030
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bcftools to GATK
... I removed indels using bcftools in 2 gvcf files. when i try to merge them using combineGVCFs/gatk, i see this error can anyone help me, how to fix this? INFO 19:05:26,829 ProgressMeter - chr22:16051001 1.6E7 30.0 s 1.0 s 53.6% 56.0 s 26.0 s ##### ERROR -- ...
snp written 8 weeks ago by GK161030 • updated 8 weeks ago by Pierre Lindenbaum107k
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Comment: C: combine gvcf error
... sed 's/\*ATCAAATG/ATCAAATG/' temp1.gvcf > temp1.flt.gvcf sed 's/\*ATCAAATG/ATCAAATG/' temp2.gvcf > temp1.flt.gvcf java -jar $GenomeAnalysisTK_jar CombineGVCFs -R $REF -V temp1.gvcf -V temp2.gvcf -O merged.gvcf I am still getting this error :( java.lang.IllegalArgumentException: Unexpected b ...
written 8 weeks ago by GK161030

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