User: BAGeno

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BAGeno70
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Posts by BAGeno

<prev • 42 results • page 1 of 5 • next >
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Comment: C: How to run bcftools roh with multiple samples vcf
... Thanks I checked and found I have bcftools 1.2 ...
written 18 days ago by BAGeno70
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Comment: C: How to run bcftools roh with multiple samples vcf
... @YaGalbi I already searched through options of bcftools roh and read bcftools manual pages but I did not see any option in bcftools roh manual in which we can specify many samples. Also I tried command with one sample name and it worked just fine. Here are the options when I tried bcftools roh help ...
written 18 days ago by BAGeno70
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Comment: C: How to run bcftools roh with multiple samples vcf
... I have tried already samples names with comma but it did not worked also I tried to run command with -S option it gave me error of `roh: invalid option -- 'S' ` ...
written 18 days ago by BAGeno70
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How to run bcftools roh with multiple samples vcf
... Hi, I am trying to run bcftools roh. I searched through this link and found it only mentioned about processing of 1000 genomes files. [Bcftools roh calling][1] My problem is this I did not know how to use this command for my file. I tried to run this command with my file it gave me this error ...
roh bcftools written 18 days ago by BAGeno70 • updated 18 days ago by finswimmer2.8k
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Comment: C: Runs of homozygosity calculation
... I have used this command vcftools --vcf Input.vcf --plink --out Plink.input It gave me both ped and map file. ...
written 19 days ago by BAGeno70
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Runs of homozygosity calculation
... Hi, I am using plink to calculate runs of homozygosity.I prepared plink format file with vcftools I ran following command plink --file Plink.input --homozyg --out Plink.result I got empty Plink.result.hom, there are headings in this file but no results. I repeated above mentioned procedure ...
roh bcftools plink written 19 days ago by BAGeno70 • updated 19 days ago by Wietje150
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Bcftools merge taking too much time and producing large file
... Hi, I have VCFs of different samples split by chromosomes. I want to merge all these chromosomes files. For this I am using this command bcftools merge --force-samples -m all *vcf.gz The size of all vcf in gz form is 230GB. But the file which is produced after merging is of 1.2TB. And it has ...
vcf bcfttools merge written 28 days ago by BAGeno70 • updated 27 days ago by Kevin Blighe21k
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CNVnator Root File
... Hi, I am new to CNVnator. I have install this tool after many problem. I run following command without any error. But I did not see any output root file. ./cnvnator /path_to_genome/hg19.fa -root /media/linux/Output.root -chrom chr22 -tree /media/linux/Input.bam Is there something wrong with m ...
cnvator cnv written 12 weeks ago by BAGeno70
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Variation and Exon number
... Hi, I have different stop gain and stop loss variants. I want to check in which exon these variants are present and whether this exons is critical for gene functions or not. How can I do this? ...
genome gene snp written 3 months ago by BAGeno70 • updated 9 weeks ago by Biostar ♦♦ 20
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Requirement of RAM for running Genome strip
... Hi, I want to perform CNV calling. I am using genome strip tool of GATK for this purpose. I found that this tool perform analysis on computer cluster, but I do not have computer cluster. Can any one tell me what are RAM requirement for running genome strip? ...
gatk cnv calling written 3 months ago by BAGeno70

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