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How to keep sample name while using samtools mpileup + varscan to do variant call?
varscan samtools mpileup written 15 days ago by MatthewP • 10 • updated 15 days ago by Pierre Lindenbaum ♦ 110k
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Varscan fpfilter error
varscan snp fpfilter bam-readcount somatic written 16 days ago by a01039012387 • 0 • updated 16 days ago by Ram ♦ 16k
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98
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Why VarScan always get more somatic variants than other caller
varscan variant written 25 days ago by CY • 140
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7 follow
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Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
varscan bioconductor copynumber written 7.0 years ago by Mdeng • 510 • updated 5 weeks ago by Kinga27 • 0
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Varscan somatic caller - Genotype calls
varscan somatic written 8 weeks ago by hshah • 20
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183
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5 follow
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Copy number variation detection
varscan copy number variation snp written 8 weeks ago by v27 • 10 • updated 8 weeks ago by d-cameron • 1.8k
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121
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varscan somatic without normal
varscan mutation written 12 weeks ago by fabbri.marco • 0
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157
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SNP/indel annotation in Arabidopsis
indel varscan arabidopsis snp written 3 months ago by Federico Giorgi • 410 • updated 3 months ago by finswimmer ♦ 3.6k
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205
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identifying TP53 germline mutations which are also in tumor cells.
somatic germline tp53 mutect varscan written 5 months ago by lait • 80 • updated 5 months ago by Noushin N • 530
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varscan copy number error
varscan cnv written 7 months ago by mittu1602 • 140
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308
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Why CNV calling using VarScan need two steps of fragments merging?
varscan copy number variant cnv written 7 months ago by CY • 140 • updated 7 months ago by arta • 490
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355
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phasing variants produced by varscan
gatk trio analysis varscan phasing variants written 7 months ago by lait • 80
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351
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Correcting SNV allele frequency
wgs varscan snv allele frequency written 8 months ago by ATpoint • 5.7k
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does varscan2 trio mode perform joint genotyoing?
trio varscan joint genotyping variant germline written 8 months ago by lait • 80
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Variant Calling in Low-Complexity Regions
indel low-complexity variants snp varscan written 9 months ago by ATpoint • 5.7k • updated 8 months ago by Biostar ♦♦ 20
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Running THetA2 with Varscan input?
varscan theta tumorpurity written 13 months ago by hshah • 20 • updated 9 months ago by j.p.albrecht • 30
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1
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500
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1
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VarScan2 Parsing Error
varscan java written 10 months ago by ATpoint • 5.7k
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Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
indel varscan tool snp written 6.2 years ago by Istvan Albert ♦♦ 77k • updated 11 months ago by AcademicDialysis • 60
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Galaxy VarScan SNP size and stderr
varscan galaxy variant bam written 12 months ago by louis.gil007 • 0
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900
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1
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SciClone on WES data
dnacopy varscan clonality wes sciclone written 14 months ago by mar.ark.parr • 30 • updated 13 months ago by Chris Miller ♦ 20k
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varscan v2.3.9 filter Parse exception
varscan written 2.1 years ago by cafelumiere12 • 70 • updated 14 months ago by jlx0248 • 0
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How to exclude noisy CNV from study?
dnacopy varscan copy number variation cnv wes written 16 months ago by rmateos.1 • 10 • updated 15 months ago by vchris_ngs • 4.5k
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Problems After Loading Varscan 2 Output Into Bioconductor.Dnacopy
exome varscan copynumber cnv sequencing written 5.4 years ago by sousuffer • 20 • updated 15 months ago by Biostar ♦♦ 20
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603
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Varscan2 filters AND usability of the tool - looking for opinions
variant calling varscan varscan2 somatic written 16 months ago by user230613 • 260
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365
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How to interpret tandem SNP in
varscan ngs dna-seq variants written 16 months ago by Paul • 1.1k
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varscan somaticFilter thinks all my variants are near INDELS so removes all of them
varscan somaticfilter false-positive filtering written 16 months ago by wes3985 • 0
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varscan2 mpileup2snp output contains indels
vcf indels mpileup2snp varscan written 2.4 years ago by AW • 350 • updated 17 months ago by Biostar ♦♦ 20
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What allele frequency threshold do you recommend?
varscan written 19 months ago by agata88 • 670 • updated 17 months ago by Biostar ♦♦ 20
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How to annotate VarScan software .snp output to see what genes have SNPs and how to make a human-readable report from that?
varscan annotation written 18 months ago by flight22121 • 10
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Different output from pileup and mpileup commands VarScan
varscan mpileup written 18 months ago by agata88 • 670
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