User: svp

gravatar for svp
svp420
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420
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Bangalore
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snijesh
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Last seen:
3 days, 10 hours ago
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1 year ago
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Posts by svp

<prev • 52 results • page 1 of 6 • next >
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Answer: A: Calling triovariants using varscan from a compressed mileup file ?
... You can try: `< zcat (file.gz)` as input varscan trio < (zcat trio.mileup.gz) trio.mpileup.output \ --min-coverage 10 --min-var-freq 0.20 --p-value 0.05 \ -adj-var-freq 0.05 -adj-p-value 0.15 ...
written 5 days ago by svp420
0
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Comment: C: Is anybody experiencing problems downloading from the SRA?
... It looks like the data is available in link ftp://ftp.sra.ebi.ac.uk/vol1/run/SRR124/SRR12492134/ when we use browser ...
written 5 days ago by svp420
2
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2
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Comment: C: How to call denovo and rare variants from a trios cohort?
... Ya, this format is correct, but you need to add `#` in the first line as: #FamID IndID PatID MatID Sex Phenotype 1 in1 Pat1 Mat1 1 2 1 Pat1 0 0 1 0 1 Mat1 0 0 2 0 2 in2 Pat2 Mat2 ...
written 7 days ago by svp420
3
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0
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Comment: C: CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
... Can you just change the line of `-ped` and try as: gatk -T CalculateGenotypePosteriors \ -R $reference \ -V trio.cohort.vcf -ped trio_cohort.ped \ -supporting-callsets $gnomad \ -o GP_triocohort.vcf ...
written 7 days ago by svp420
0
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3
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Comment: C: Combine two VCF files with GATK4
... `MergeVcfs` of `gatk` will not work with different entries ...
written 7 days ago by svp420
3
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3
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116
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3
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Answer: A: Combine two VCF files with GATK4
... Try using snpsift `java -jar SnpSift.jar split -j *.vcf > combined.vcf` ...
written 7 days ago by svp420
2
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0
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Comment: C: How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
... If you look into the [this][1] tutorial `Note that mixed records are treated as indels.` [1]: https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator ...
written 7 days ago by svp420
0
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Comment: C: GATK4 VariantRecalibrator resource error
... when you referring to latest, it would be nice to put the version name also ...
written 9 days ago by svp420
1
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1
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Comment: C: How to call denovo variants from multiple trios cohort?
... This format seems correct. You can also go through this [link][1] [1]: https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format ...
written 14 days ago by svp420
1
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Answer: A: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
... Remove all the rows which have `0` values across the samples You may have all the rows having `0` values in the dataframe ...
written 8 weeks ago by svp420

Latest awards to svp

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Web scraping in the KEGG db
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Combine two VCF files with GATK4
Voter 19 days ago, voted more than 100 times.
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Why 'filterByExpr' does not eliminate low read counts from the expression data?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Web scraping in the KEGG db
Supporter 6 months ago, voted at least 25 times.

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