User: nitinra

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Posts by nitinra

<prev • 7 results • page 1 of 1 • next >
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Negative Fst values from VCFtools result
... Hello all, I am calculating Fst using VCFtools and here is the code I am running: vcftools --vcf input.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out pop1_pop2 I am getting the mean fst value in negative: -0.0003 (I did expect it to be low since they are very close), but a lot of ...
genome vcftool fst snp written 20 days ago by nitinra0 • updated 20 days ago by genomax91k
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Comment: C: Handing scafflold names for plink bed file
... I did and the analysis runs. however, It shows up as an error when I use it in admixture since the names are still present for scaffolds. ...
written 20 days ago by nitinra0
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Handing scafflold names for plink bed file
... Hello all, I am trying to convert vcf file to bed file using plink pipeline. I used the following command: `plink --vcf input.vcf --make-bed --o output` However, I had to change the names of my chromosomes to just numbers using awk command: awk '{gsub(/^Chromosome_/,""); print}' no_chr1.vcf & ...
bedfile genome plink snp written 21 days ago by nitinra0 • updated 21 days ago by genomax91k
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Error while merging multiple vcf files using Picard MergeVcfs
... Hello all, I am trying to merge multiple vcf files using MergeVcfs from Picard tools. Here is my command: java -jar ./picard.jar I=input1.vcf I=input2.vcf I=inputx.vcf O=combined.vcf However, I am getting the following error: > Input file .vcf has sample entries that don't match the oth ...
genome gatk picard tool snp written 22 days ago by nitinra0 • updated 22 days ago by Medhat8.8k
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merging multiple vcfs by column in Picard
... Hello everyone, I used `picard MergeVcfs` to combine individual vcf files with the following command: java -jar /picard.jar MergeVcfs -I input.vcf -I input2.vcf -I inputs.vcf O= output.vcf.gz The resulting output file looks like this: #CHROM POS ID REF ALT QUAL FI ...
vcf genome picard snp written 26 days ago by nitinra0 • updated 26 days ago by Pierre Lindenbaum131k
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Bedtools merge messing chromosome start - end points
... Hello everyone, I am trying to merge my `bedtools genomecov` output using the `bedtools merge` option. I am using this data : Chromosome_1 0 54 0 Chromosome_1 54 204 3 Chromosome_1 204 410 0 Chromosome_1 410 476 2 Chromosome_1 476 502 4 .... I used the following command to r ...
genome bedtools merge merge bedtools written 4 weeks ago by nitinra0 • updated 25 days ago by Jorge Amigo12k
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Plotting large file size of bedtools genomecov output
... Hi everyone, I generated the output for coverage using bedrolls genomecov using this command: bedtools genomecov -ibam input.sorted.bam > output.coverage -bga The resulting files are huge (range of 5-6gb/file). I do not think it is possible for me to use R to plot the histogram since it ...
bedtools genomecov genome coverage depth written 4 weeks ago by nitinra0 • updated 4 weeks ago by Pierre Lindenbaum131k

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