User: BAGeno

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BAGeno110
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Posts by BAGeno

<prev • 62 results • page 1 of 7 • next >
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Failed to liftover from hg38 to hg19
... Hi, I am converting my file from hg38 to hg19. For this purpose I used `crossmap` and `picard LiftoverVcf`. But I am getting this error when I run `crossmap`. Traceback (most recent call last): File "/home/linux/anaconda3/bin/CrossMap.py", line 1760, in crossmap_vcf_file(mapping ...
crossmap picard written 8 weeks ago by BAGeno110
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Annovar and VEP overlapp
... Hi, I want to check VEP and annovar overlap that is how many variants are annotated same by both of these tools. But I don't how to do it as VEP output contain many transcripts and so there is difference in number of annotations done by both these tools. So what do you suggest I should perform the ...
annovar vep written 9 weeks ago by BAGeno110 • updated 9 weeks ago by Kevin Blighe37k
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Comment: C: Vep loftool threshold
... I want to separate probably damaging variants from output. So what value should I used to separate these variants? ...
written 10 weeks ago by BAGeno110
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Vep loftool threshold
... Hi, I have annotated my file with vep loftool. I want to find out what is threshold used by vep loftool to assign variants as probably damaging, possibly damaging or benign? I know that more lower score more intolerant s variant is but what is criteria to rank variants. Also I want to know that is ...
loftool vep written 10 weeks ago by BAGeno110 • updated 10 weeks ago by Emily_Ensembl17k
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Comment: C: PharmGKB haplotype table
... I have only have phased vcf as I did not called variants so I does not have genotype for every position. Is there no way to do this kind of work with vcf? ...
written 4 months ago by BAGeno110
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Comment: C: PharmGKB haplotype table
... @Kevin I was wondering what about position in which no variant is found. In processing my data I found all variants from above mentioned haplotype except `rs3212200`. Does this means that on location in which this variant is found there was reference allele which was `T`?. As without considering unc ...
written 4 months ago by BAGeno110
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PharmGKB haplotype table
... Hi, Does any one know on what base does PharmGKB decide haplotype reference allele?. I checked different snps in dbsnp the reference alleles are not same in Pharmgkb haplotype table and that of dbsnp like `rs3818247 ` reference allele in dbsnp is `G` but in PharmGKB haplotype table of `HNF4A` refer ...
gene pharmgkb dbsnp snp written 4 months ago by BAGeno110 • updated 4 months ago by Kevin Blighe37k
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Haplotype analysis from phased vcf
... Hi, I want to ask that how can I perform haplotype analysis from phased vcf. I have vcf in this format. #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4 S5 S6 10 94870 rs123 A G 30 PASS AN=20;AC=11 ...
vcf haplotype phased written 4 months ago by BAGeno110
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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 5 months ago by BAGeno110
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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 5 months ago by BAGeno110 • updated 10 weeks ago by Mehulsharma.25310

Latest awards to BAGeno

Popular Question 29 days ago, created a question with more than 1,000 views. For EBI SRA FTP is not working
Popular Question 11 weeks ago, created a question with more than 1,000 views. For VEP and Annovar Annotation
Popular Question 4 months ago, created a question with more than 1,000 views. For Grep Position List

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