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<prev • 120 results • page 1 of 4 • next >
8
votes
1
answer
2.8k
views
1
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Problem Analyzing Tumor-Normal Pairs With Varscan
varscan next-gen samtools cancer written 8.3 years ago by tommivat • 240 • updated 7 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
122
views
0
answers
question of varscan filter
varscan snp written 3 months ago by duolin1 • 10
0
votes
2
answers
3.9k
views
2
answers
Using Samtools mpileup with Varscan
varscan next-gen samtools rna-seq written 5.3 years ago by Ron • 1.0k • updated 3 months ago by field654 • 10
0
votes
0
answers
112
views
0
answers
varscan - how to calculate MinMMQSdiff
varscan minmmqsdiff bam-readcount written 4 months ago by reany • 0
0
votes
0
answers
135
views
0
answers
ADR, ADF and dp4 counts do not count strands correct
lofreq varscan mutation sequencing written 5 months ago by g.t.los • 0
0
votes
0
answers
164
views
0
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include vcf header
varscan written 9 months ago by archie • 100
1
vote
2
answers
510
views
2
answers
Copy number profile using VarScan
varscan cnv_graph cnvs R written 12 months ago by tanbiswas6 • 0
0
votes
0
answers
245
views
0
answers
merge segment using varscan
varscan cnvs merge_segments written 12 months ago by tanbiswas6 • 0
0
votes
0
answers
331
views
0
answers
How rare are somatic mutations?
varscan tumor mutect snp somatic written 13 months ago by syntax • 60
0
votes
0
answers
386
views
0
answers
Understanding the output of pileup2snp
variant samtools snp varscan written 15 months ago by e.rempel • 970 • updated 13 months ago by Biostar ♦♦ 20
1
vote
0
answers
248
views
0
answers
how generated haploid variants by varscan
indel varscan haploid snp written 14 months ago by kamel • 30
1
vote
1
answer
505
views
1
answer
VarScan.v2.4.3 generating incomplete or partial VCF file
variant calling exomeseq snp varscan written 16 months ago by Sandeep • 260 • updated 16 months ago by 2nelly • 220
4
votes
1
answer
553
views
1
answer
Using Varscan without a matched normal
varscan wes written 16 months ago by sugus • 50 • updated 16 months ago by Chris Miller ♦ 21k
0
votes
0
answers
434
views
0
answers
varscan tool for copy number variation detection
varscan next-gen sequencing written 17 months ago by nesmaabdelaziz60 • 0
0
votes
1
answer
470
views
1
answer
can VarScan2 do joint somatic calling?
varscan somatic calling snp written 19 months ago by Zoey Zou • 40
1
vote
0
answers
717
views
0
answers
Running time in different callers
varscan snv mutect wgs written 19 months ago by A • 3.9k
2
votes
2
answers
2.1k
views
2
answers
Finding SNPs per gene for SNP Density in UNIX
varscan grep unix snp written 5.1 years ago by crawlthrutacos • 0 • updated 19 months ago by Biostar ♦♦ 20
6
votes
1
answer
2.0k
views
1
answer
Gold Standard for Human cancer exome sequencing
somatic wes varscan mutect cancer written 4.1 years ago by Jerome Lin • 20 • updated 20 months ago by Biostar ♦♦ 20
0
votes
2
answers
433
views
2
answers
bam-readcount error Expect Library
varscan snp bam-readcount sequencing written 20 months ago by 9521ljh • 20 • updated 20 months ago by Pierre Lindenbaum ♦ 131k
4
votes
0
answers
1.7k
views
0
answers
Problem in converting vcf to maf using vcf2maf tools
varscan grch38 vcf2maf written 21 months ago by Rahil • 180
2
votes
1
answer
625
views
1
answer
How to annotate Copy Number Variations (Output of VarScan2)
varscan cnv annotation written 21 months ago by Rahil • 180 • updated 21 months ago by Pierre Lindenbaum ♦ 131k
2
votes
1
answer
913
views
1
answer
VarScan: How is the DP score in a .vcf calculated?
vcf varscan written 22 months ago by James Reeve • 100 • updated 22 months ago by igor ♦ 11k
3
votes
1
answer
578
views
1
answer
Can a normal tissue sequence be used for various tumor samples in Varscan Somatic or GATK MuTect2?
gatk varscan mutect2 written 22 months ago by tarekzakaria.badr • 30 • updated 22 months ago by Charles Warden ♦ 7.9k
0
votes
0
answers
414
views
0
answers
Can I use VarScan for tumor_time2/tumor_time1 CNA and SNP calling?
cna varscan cnv snp written 24 months ago by Pin.Bioinf • 270 • updated 23 months ago by Biostar ♦♦ 20
11
votes
1
answer
7.1k
views
8 follow
1
answer
Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
varscan bioconductor copynumber written 9.3 years ago by Mdeng • 510 • updated 24 months ago by noonbobnoon • 10
0
votes
0
answers
541
views
0
answers
Error in normalizing lines of sequence in a fasta file using NormalizeFasta (Picard)
normalizefasta picard bam-readcount varscan written 2.0 years ago by Rahil • 180
1
vote
1
answer
767
views
1
answer
Finding somatic and germline variations in tumor samples with matched ones (paired-end, illumina)
varscan wes data mpileup file written 2.0 years ago by Rahil • 180 • updated 2.0 years ago by ATpoint ♦ 41k
0
votes
0
answers
609
views
0
answers
Problem understanding GT from Varscan's vcf output
varscan written 2.1 years ago by ww22runner • 0 • updated 2.1 years ago by RamRS ♦ 30k
1
vote
1
answer
602
views
1
answer
How to Interpret Deletions from varscan?
variants varscan indels alignment deletion written 2.1 years ago by athulmenonk • 0
2
votes
1
answer
792
views
1
answer
Calling somatic variants with Varscan
varscan written 2.1 years ago by ww22runner • 0
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