User: BAGeno

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BAGeno80
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Posts by BAGeno

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Temporary Directory Problem in GATK4
... I am using /bin/bash. I have set whole path to tmp directory. And there was space in `export_JAVA_OPTIONS=-Djava.io.tmpdir=./tmp` which I removed but now it is giving me error A USER ERROR has occurred: 'export_JAVA_OPTIONS=-Djava.io.tmpdir=./tmp' is not a valid command. ...
written 19 days ago by BAGeno80
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Temporary Directory Problem in GATK4
... Hi, I have recently shifted from GATK 3 to GATK4. It has changed very much. I figured most of the step but one thing is giving me problem is that how to set temporary directory option in GATK4. I have used this option `export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp ` with this option `--TMP_DIR ./tmp/ ...
gatk4 directory java temporary written 19 days ago by BAGeno80 • updated 19 days ago by dariober9.4k
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How to check which samples has more uncalled genotypes in multi-sample vcf
... Hi, I have multi-sample vcf and in this vcf, there are many sites which have uncalled or missing genotype. Is there a way to check which sample has greater number of uncalled genotypes in vcf. So that I can exclude that sample from further analysis. ...
missing sample genotype written 7 weeks ago by BAGeno80 • updated 7 weeks ago by Pierre Lindenbaum112k
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Comment: C: Problem with allele number in vcf
... I want to do population analysis. whether a certain disease variants is present in the population or not. Also can you please tell me should you I check this? > how many samples have no calls in regions where that variant was found ...
written 8 weeks ago by BAGeno80
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Comment: C: Problem with allele number in vcf
... I have ./. in my vcf. Should I remove these calls from my vcf. I have do different population analysis. I did not called variants so I cannot do anything on that step. ...
written 8 weeks ago by BAGeno80
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Problem with allele number in vcf
... Hi, I have vcf of 1000 samples. But I am facing the problem that I have different allele number of every site in vcf. There are some samples which have dots instead of 0 and 1 in genotype column. Can any one please tell me how should in correct the problem of different allele number? ...
vcf genotype allele number written 8 weeks ago by BAGeno80 • updated 8 weeks ago by aheinzel110
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Comment: C: Location of intronic SNPs from exons
... @cpad0112 I tried your suggestion. And got something like this. `HGVSc=ENST00000234961.6:c.228-10520A>C` Could you please explain this? ...
written 9 weeks ago by BAGeno80
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Finding overlapping regions in two file along with their associated information
... Hi, I have two file in which there are chromosomes positions and other information. I want to find their overlapping regions for this purpose I used bedtools. And I got overlapping coordinates between both files. Now I want file in which I have other information from both files associated with over ...
bedtools genes overlapping regions written 9 weeks ago by BAGeno80
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Location of intronic SNPs from exons
... Hi, I have list of intronic SNPs. I used VEPP to find in which intron a specific SNP is located. But I want to find how many base pairs is that intronic SNP away from exon. Is there a tool to do this? ...
vep exon introns position written 9 weeks ago by BAGeno80 • updated 9 weeks ago by Emily_Ensembl15k
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Comment: C: Exonic SNPs extraction
... If you have rs number then may be you can use annotation based tools like wAnnovar, SNP nexus or VEP. These will exonic SNPs. ...
written 11 weeks ago by BAGeno80

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