User: GK1610

gravatar for GK1610
GK161080
Reputation:
80
Status:
Trusted
Location:
United States
Last seen:
5 days, 10 hours ago
Joined:
3 years, 11 months ago
Email:
k****************@gmail.com

Posts by GK1610

<prev • 53 results • page 1 of 6 • next >
1
vote
0
answers
48
views
0
answers
Rat Genome and dbsnp file
... From where can I download rat dbsnp and indels VCF file? I have the genome for Rattus norvegicus v6 ...
genome written 5 days ago by GK161080
0
votes
0
answers
71
views
0
answers
Structural Variants in a VCF file
... I have a vcf file of WGS of 100 samples. I want to check how many samples have e.g. deletion or duplication for a given region chrX:1-1000. What are the steps to get no of samples with SVs ( text file)? ...
snp written 18 days ago by GK161080
0
votes
0
answers
300
views
0
answers
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 15 months ago by GK161080 • updated 13 months ago by Biostar ♦♦ 20
0
votes
1
answer
397
views
1
answer
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 16 months ago by GK161080
1
vote
1
answer
1.1k
views
1
answer
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 16 months ago by GK161080 • updated 16 months ago by swbarnes27.9k
0
votes
0
answers
417
views
0
answers
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 16 months ago by GK161080 • updated 15 months ago by Biostar ♦♦ 20
0
votes
3
answers
1.6k
views
3
answers
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 16 months ago by GK161080
1
vote
1
answer
591
views
1
answer
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 16 months ago by GK161080 • updated 9 months ago by Biostar ♦♦ 20
4
votes
1
answer
380
views
1
answer
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 16 months ago by GK161080
1
vote
0
answers
1.2k
views
0
answers
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 21 months ago by GK161080

Latest awards to GK1610

Popular Question 18 days ago, created a question with more than 1,000 views. For GATK GenotypeGVCFs output is empty gvcf file
Popular Question 13 months ago, created a question with more than 1,000 views. For GATK GenotypeGVCFs output is empty gvcf file
Popular Question 13 months ago, created a question with more than 1,000 views. For Find Fragment Size of a bamfilee
Popular Question 13 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 13 months ago, created a question with more than 1,000 views. For randomly subsampling a bam file three times
Popular Question 13 months ago, created a question with more than 1,000 views. For From bed file to enrichment score
Popular Question 13 months ago, created a question with more than 1,000 views. For MACS2 Nomodel doesnt take the fragment size
Popular Question 13 months ago, created a question with more than 1,000 views. For bcftools concatenation error
Popular Question 19 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 2.3 years 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 2.3 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 2.7 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 2.7 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 2.7 years ago, created a question with more than 1,000 views. For randomly subsampling a bam file three times

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1656 users visited in the last hour