User: GK1610

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GK161060
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Posts by GK1610

<prev • 51 results • page 1 of 6 • next >
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to check allelic biases in histone peaks
... I have called QTLs on histone peaks if I want to see if hQTLs that are located inside the histone peaks exhibits allelic biases or not? How do I do it? What I have done is as following: 1) I took peaks for which hQTLs-snps is inside the peak 2) for hQTL-snps, peaks combination, I found set of indi ...
chip-seq snp written 6 months ago by GK161060 • updated 4 months ago by Biostar ♦♦ 20
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GC content from bam to fasta file
... I want to get mean_gc content of a given bed regions from a bam file I use samtools fasta $bam > $bam.fasta bedtools nuc -fi $bam.fasta -bed $regions.bed >$bam_gc_content.bed this gives me the error 1:67000041-67000044) beyond the length of chr1 size (0 bp). Skipping. my regions.b ...
chip-seq written 7 months ago by GK161060
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bcftools concatenation error
... I have 22 vcf files from each chromosomes. I am try ing to concatenate the vcf files bcftools concat -f files.txt -Oz > merged.vcf I keep getting this error: > chromosome 9 is not contiguous, consider running with -a. How can I resolve this issue? ...
bcftools snp written 7 months ago by GK161060 • updated 7 months ago by swbarnes26.7k
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QTLtools pca detects no varaints
... Hi I have two vcf files from different sets of individuals 1.vcf file is genotype data and 2.vcf files is wgs data when I run QTLtools pca --vcf 1.vcf --scale --center --maf 0.05 --distance 50000 --out 1.genotypes.output QTLtools pca --vcf 2.vcf --scale --center --maf 0.05 --distance 500 ...
snp written 8 months ago by GK161060 • updated 6 months ago by Biostar ♦♦ 20
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Answer: A: Updating allele frequency (AF) and minor allele frequency (MAF) INFO fields in .
... when I run this , I get the following error VCF=unzipped_vcf_file awk '/^#CHROM/ {printf("##INFO=\n##INFO=\n");} {print}' $VCF |\ java -jar /sc/orga/projects/psychencode/kiran/jvarkit/dist/vcffilterjdk.jar -e 'VariantContextBuilder vcb = new VariantContextBuilder(variant); float ac = variant.getA ...
written 8 months ago by GK161060
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Merge WGS and genotype data
... I have a genotype data vcf file of 100 individuals filtered for maf >.01 and then I take wgs file of another 50 individuals and I intersect the sites that are common in both genotype and wgs data. I merge the wgs and genotype data for these common sites using bcftools This new merged vcf file ...
snp written 8 months ago by GK161060 • updated 12 days ago by Biostar ♦♦ 20
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variants filtering with maf>5% every 100kb
... I have a genotype vcf file for which I want to do trimming such that I have one variant with MAF > 5% every 100kb. Does anyone have suggestions to do this smartly using bcftools or vcftools ? Thanks Kiran ...
snp written 8 months ago by GK161060
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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 12 months ago by GK161060
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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 12 months ago by GK161060 • updated 12 months 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 13 months ago by GK161060

Latest awards to GK1610

Popular Question 11 months ago, created a question with more than 1,000 views. For How to remove duplicates in a sorted bam file using picard?
Popular Question 19 months ago, created a question with more than 1,000 views. For How can I increase the number of peaks using macs2 peak caller?
Popular Question 19 months ago, created a question with more than 1,000 views. For How can I save the output from samtools and awk as a bam file?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How can I save the output from samtools and awk as a bam file?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to remove duplicates in a sorted bam file using picard?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For randomly subsampling a bam file three times

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