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2
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VarScan2 Parsing Error
varscan java written 4 days ago by ATPoint • 1.1k
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1.7k
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Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
indel varscan tool snp written 5.4 years ago by Istvan Albert ♦♦ 73k • updated 5 weeks ago by AcademicDialysis • 60
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167
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Galaxy VarScan SNP size and stderr
varscan galaxy variant bam written 9 weeks ago by louis.gil007 • 0
1
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1
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343
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1
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SciClone on WES data
dnacopy varscan clonality wes sciclone written 4 months ago by mar.ark.parr • 30 • updated 3 months ago by Chris Miller ♦ 18k
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141
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Running THetA2 with Varscan input?
varscan theta tumorpurity written 3 months ago by hshah • 0
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1
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705
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1
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varscan v2.3.9 filter Parse exception
varscan written 15 months ago by cafelumiere12 • 70 • updated 4 months ago by jlx0248 • 0
1
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1
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297
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1
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How to exclude noisy CNV from study?
dnacopy varscan copy number variation cnv wes written 6 months ago by rmateos.1 • 10 • updated 5 months ago by vchris_ngs • 4.0k
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Problems After Loading Varscan 2 Output Into Bioconductor.Dnacopy
exome varscan copynumber cnv sequencing written 4.5 years ago by sousuffer • 20 • updated 5 months ago by Biostar ♦♦ 20
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315
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Varscan2 filters AND usability of the tool - looking for opinions
variant calling varscan varscan2 somatic written 6 months ago by user230613 • 240
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184
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How to interpret tandem SNP in
varscan ngs dna-seq variants written 6 months ago by Paul • 650
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309
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varscan somaticFilter thinks all my variants are near INDELS so removes all of them
varscan somaticfilter false-positive filtering written 6 months ago by wes3985 • 0
1
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624
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varscan2 mpileup2snp output contains indels
vcf indels mpileup2snp varscan written 18 months ago by AW • 280 • updated 7 months ago by Biostar ♦♦ 20
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493
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What allele frequency threshold do you recommend?
varscan written 9 months ago by agata88 • 610 • updated 7 months ago by Biostar ♦♦ 20
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339
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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 7 months ago by flight22121 • 10
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1
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369
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1
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Different output from pileup and mpileup commands VarScan
varscan mpileup written 8 months ago by agata88 • 610
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How to output VarsScan variant calling results in a .tab or txt/csv file?
varscan variant calling samtools written 8 months ago by vassialkalive23 • 0
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590
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What is genotype quality scale?
varscan quality genotype written 9 months ago by agata88 • 610
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Exome-seq; Which tools to predict significantly muated genes .
varscan music cnv written 10 months ago by Chirag Nepal • 1.9k • updated 10 months ago by Biostar ♦♦ 20
6
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1
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555
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1
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Gold Standard for Human cancer exome sequencing
somatic wes varscan mutect cancer written 10 months ago by Jerome Lin • 20 • updated 10 months ago by harold.smith.tarheel • 3.8k
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244
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Varscan mpileup2snp coverage filter
mpileup2snp varscan written 10 months ago by AW • 280
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402
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Varscan mpileup2snp parameters
mpileup2snp varscan snpcalling written 10 months ago by AW • 280
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1
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538
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1
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Variant Calling in Somatic mode
vcf varscan variants snp sequencing written 10 months ago by Paul • 650 • updated 10 months ago by venu • 4.3k
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1
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646
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1
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sciClone:input data wrong
dnacopy varscan copy number sciclone cluster written 11 months ago by lyan.liu • 0 • updated 11 months ago by Chris Miller ♦ 18k
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1
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646
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1
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indel preprocessing prior to bam-readcount
indel varscan fpfilter.pl bam-readcount written 11 months ago by Jokhe • 40 • updated 11 months ago by m.b • 0
0
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2
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768
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Finding SNPs per gene for SNP Density in UNIX
varscan grep unix snp written 22 months ago by crawlthrutacos • 0 • updated 13 months ago by Alex Reynolds ♦ 20k
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455
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a problem with varscan
software error varscan samtools mpileup written 13 months ago by ZoeChing • 0
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1
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1.2k
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1
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VarScan and Samtools - how to process my data?
varscan ngs sequencing samtools pipeline written 13 months ago by ciemanek • 20 • updated 13 months ago by poisonAlien • 2.4k
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585
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Clear explanation of parameter minReads2 in VarScan
vcf varscan sequencing written 14 months ago by John • 60
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543
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Varscan variant calll error on pacbio data
varscan blasr mpileup pacbio written 15 months ago by mark.rose • 10
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2
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Non-cancer somatic mutation calling
varscan samtools somatic mutations mutect gatk written 16 months ago by Helene • 390
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